1
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Zhang L, Dopfer-Jablonka A, Cossmann A, Stankov MV, Graichen L, Moldenhauer AS, Fichter C, Aggarwal A, Turville SG, Behrens GM, Pöhlmann S, Hoffmann M. Rapid spread of the SARS-CoV-2 JN.1 lineage is associated with increased neutralization evasion. iScience 2024; 27:109904. [PMID: 38812550 PMCID: PMC11134884 DOI: 10.1016/j.isci.2024.109904] [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: 01/23/2024] [Revised: 04/16/2024] [Accepted: 05/01/2024] [Indexed: 05/31/2024] Open
Abstract
In July/August 2023, the highly mutated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) BA.2.86 lineage emerged and its descendant JN.1 is on track to become the dominant SARS-CoV-2 lineage globally. Compared to the spike (S) protein of the parental BA.2.86 lineage, the JN.1 S protein contains one mutation, L455S, which may affect receptor binding and antibody evasion. Here, we performed a virological assessment of the JN.1 lineage employing pseudovirus particles bearing diverse SARS-CoV-2 S proteins. Using this strategy, it was found that S protein mutation L455S confers increased neutralization resistance but reduces ACE2 binding capacity and S protein-driven cell entry efficiency. Altogether, these data suggest that the benefit of increased antibody evasion outweighs the reduced ACE2 binding capacity and further enabled the JN.1 lineage to effectively spread in the human population.
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Affiliation(s)
- Lu Zhang
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Alexandra Dopfer-Jablonka
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany
| | - Anne Cossmann
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Metodi V. Stankov
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Luise Graichen
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | | | - Christina Fichter
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Anupriya Aggarwal
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Stuart G. Turville
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Georg M.N. Behrens
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany
- Center for Individualized Infection Medicine (CiiM), Hannover, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
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2
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Zhang L, Dopfer-Jablonka A, Nehlmeier I, Kempf A, Graichen L, Calderón Hampel N, Cossmann A, Stankov MV, Morillas Ramos G, Schulz SR, Jäck HM, Behrens GMN, Pöhlmann S, Hoffmann M. Virological Traits of the SARS-CoV-2 BA.2.87.1 Lineage. Vaccines (Basel) 2024; 12:487. [PMID: 38793739 PMCID: PMC11125805 DOI: 10.3390/vaccines12050487] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/21/2024] [Accepted: 04/28/2024] [Indexed: 05/26/2024] Open
Abstract
Transmissibility and immune evasion of the recently emerged, highly mutated SARS-CoV-2 BA.2.87.1 are unknown. Here, we report that BA.2.87.1 efficiently enters human cells but is more sensitive to antibody-mediated neutralization than the currently dominating JN.1 variant. Acquisition of adaptive mutations might thus be needed for efficient spread in the population.
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Affiliation(s)
- Lu Zhang
- Infection Biology Unit, German Primate Center—Leibniz Institute for Primate Research, 37077 Göttingen, Germany; (L.Z.); (I.N.); (A.K.); (L.G.); (S.P.)
- Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Alexandra Dopfer-Jablonka
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.D.-J.); (N.C.H.); (A.C.); (M.V.S.); (G.M.R.); (G.M.N.B.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 30625 Hannover, Germany
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center—Leibniz Institute for Primate Research, 37077 Göttingen, Germany; (L.Z.); (I.N.); (A.K.); (L.G.); (S.P.)
| | - Amy Kempf
- Infection Biology Unit, German Primate Center—Leibniz Institute for Primate Research, 37077 Göttingen, Germany; (L.Z.); (I.N.); (A.K.); (L.G.); (S.P.)
- Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Luise Graichen
- Infection Biology Unit, German Primate Center—Leibniz Institute for Primate Research, 37077 Göttingen, Germany; (L.Z.); (I.N.); (A.K.); (L.G.); (S.P.)
- Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Noemí Calderón Hampel
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.D.-J.); (N.C.H.); (A.C.); (M.V.S.); (G.M.R.); (G.M.N.B.)
| | - Anne Cossmann
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.D.-J.); (N.C.H.); (A.C.); (M.V.S.); (G.M.R.); (G.M.N.B.)
| | - Metodi V. Stankov
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.D.-J.); (N.C.H.); (A.C.); (M.V.S.); (G.M.R.); (G.M.N.B.)
| | - Gema Morillas Ramos
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.D.-J.); (N.C.H.); (A.C.); (M.V.S.); (G.M.R.); (G.M.N.B.)
| | - Sebastian R. Schulz
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany (H.-M.J.)
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany (H.-M.J.)
| | - Georg M. N. Behrens
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.D.-J.); (N.C.H.); (A.C.); (M.V.S.); (G.M.R.); (G.M.N.B.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 30625 Hannover, Germany
- Center for Individualized Infection Medicine (CiiM), 30625 Hannover, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center—Leibniz Institute for Primate Research, 37077 Göttingen, Germany; (L.Z.); (I.N.); (A.K.); (L.G.); (S.P.)
- Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center—Leibniz Institute for Primate Research, 37077 Göttingen, Germany; (L.Z.); (I.N.); (A.K.); (L.G.); (S.P.)
- Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
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3
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Bley H, Krisp C, Schöbel A, Hehner J, Schneider L, Becker M, Stegmann C, Heidenfels E, Nguyen-Dinh V, Schlüter H, Gerold G, Herker E. Proximity labeling of host factor ANXA3 in HCV infection reveals a novel LARP1 function in viral entry. J Biol Chem 2024; 300:107286. [PMID: 38636657 PMCID: PMC11101947 DOI: 10.1016/j.jbc.2024.107286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/20/2024] Open
Abstract
Hepatitis C virus (HCV) infection is tightly connected to the lipid metabolism with lipid droplets (LDs) serving as assembly sites for progeny virions. A previous LD proteome analysis identified annexin A3 (ANXA3) as an important HCV host factor that is enriched at LDs in infected cells and required for HCV morphogenesis. To further characterize ANXA3 function in HCV, we performed proximity labeling using ANXA3-BioID2 as bait in HCV-infected cells. Two of the top proteins identified proximal to ANXA3 during HCV infection were the La-related protein 1 (LARP1) and the ADP ribosylation factor-like protein 8B (ARL8B), both of which have been previously described to act in HCV particle production. In follow-up experiments, ARL8B functioned as a pro-viral HCV host factor without localizing to LDs and thus likely independent of ANXA3. In contrast, LARP1 interacts with HCV core protein in an RNA-dependent manner and is translocated to LDs by core protein. Knockdown of LARP1 decreased HCV spreading without altering HCV RNA replication or viral titers. Unexpectedly, entry of HCV particles and E1/E2-pseudotyped lentiviral particles was reduced by LARP1 depletion, whereas particle production was not altered. Using a recombinant vesicular stomatitis virus (VSV)ΔG entry assay, we showed that LARP1 depletion also decreased entry of VSV with VSV, MERS, and CHIKV glycoproteins. Therefore, our data expand the role of LARP1 as an HCV host factor that is most prominently involved in the early steps of infection, likely contributing to endocytosis of viral particles through the pleiotropic effect LARP1 has on the cellular translatome.
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Affiliation(s)
- Hanna Bley
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Christoph Krisp
- Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anja Schöbel
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Julia Hehner
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Laura Schneider
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Miriam Becker
- Institute for Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hanover, Hanover, Germany
| | - Cora Stegmann
- Institute for Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hanover, Hanover, Germany
| | - Elisa Heidenfels
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Van Nguyen-Dinh
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Hartmut Schlüter
- Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gisa Gerold
- Institute for Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hanover, Hanover, Germany; Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Eva Herker
- Institute of Virology, Philipps-University Marburg, Marburg, Germany.
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4
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Kulma M, Šakanović A, Bedina-Zavec A, Caserman S, Omersa N, Šolinc G, Orehek S, Hafner-Bratkovič I, Kuhar U, Slavec B, Krapež U, Ocepek M, Kobayashi T, Kwiatkowska K, Jerala R, Podobnik M, Anderluh G. Sequestration of membrane cholesterol by cholesterol-binding proteins inhibits SARS-CoV-2 entry into Vero E6 cells. Biochem Biophys Res Commun 2024; 716:149954. [PMID: 38704887 DOI: 10.1016/j.bbrc.2024.149954] [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: 02/13/2024] [Revised: 03/26/2024] [Accepted: 04/15/2024] [Indexed: 05/07/2024]
Abstract
Membrane lipids and proteins form dynamic domains crucial for physiological and pathophysiological processes, including viral infection. Many plasma membrane proteins, residing within membrane domains enriched with cholesterol (CHOL) and sphingomyelin (SM), serve as receptors for attachment and entry of viruses into the host cell. Among these, human coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), use proteins associated with membrane domains for initial binding and internalization. We hypothesized that the interaction of lipid-binding proteins with CHOL in plasma membrane could sequestrate lipids and thus affect the efficiency of virus entry into host cells, preventing the initial steps of viral infection. We have prepared CHOL-binding proteins with high affinities for lipids in the plasma membrane of mammalian cells. Binding of the perfringolysin O domain four (D4) and its variant D4E458L to membrane CHOL impaired the internalization of the receptor-binding domain of the SARS-CoV-2 spike protein and the pseudovirus complemented with the SARS-CoV-2 spike protein. SARS-CoV-2 replication in Vero E6 cells was also decreased. Overall, our results demonstrate that the integrity of CHOL-rich membrane domains and the accessibility of CHOL in the membrane play an essential role in SARS-CoV-2 cell entry.
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Affiliation(s)
- Magdalena Kulma
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Aleksandra Šakanović
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Apolonija Bedina-Zavec
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Simon Caserman
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Neža Omersa
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Gašper Šolinc
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Sara Orehek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Iva Hafner-Bratkovič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia
| | - Urška Kuhar
- Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000, Ljubljana, Slovenia
| | - Brigita Slavec
- Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000, Ljubljana, Slovenia
| | - Uroš Krapež
- Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000, Ljubljana, Slovenia
| | - Matjaž Ocepek
- Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000, Ljubljana, Slovenia
| | - Toshihide Kobayashi
- Lipid Biology Laboratory, RIKEN, 2-1, Hirosawa, Wako-shi, Saitama, 351-0198, Japan; UMR 7021 CNRS, Université de Strasbourg, F-67401, Illkirch, France
| | - Katarzyna Kwiatkowska
- Laboratory of Molecular Membrane Biology, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, 3 Pasteur St., 02-093, Warsaw, Poland
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia.
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5
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Bigotti MG, Klein K, Gan ES, Anastasina M, Andersson S, Vapalahti O, Katajisto P, Erdmann M, Davidson AD, Butcher SJ, Collinson I, Ooi EE, Balistreri G, Brancaccio A, Yamauchi Y. The α-dystroglycan N-terminus is a broad-spectrum antiviral agent against SARS-CoV-2 and enveloped viruses. Antiviral Res 2024; 224:105837. [PMID: 38387750 DOI: 10.1016/j.antiviral.2024.105837] [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: 11/24/2023] [Revised: 01/20/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
The COVID-19 pandemic has shown the need to develop effective therapeutics in preparedness for further epidemics of virus infections that pose a significant threat to human health. As a natural compound antiviral candidate, we focused on α-dystroglycan, a highly glycosylated basement membrane protein that links the extracellular matrix to the intracellular cytoskeleton. Here we show that the N-terminal fragment of α-dystroglycan (α-DGN), as produced in E. coli in the absence of post-translational modifications, blocks infection of SARS-CoV-2 in cell culture, human primary gut organoids and the lungs of transgenic mice expressing the human receptor angiotensin I-converting enzyme 2 (hACE2). Prophylactic and therapeutic administration of α-DGN reduced SARS-CoV-2 lung titres and protected the mice from respiratory symptoms and death. Recombinant α-DGN also blocked infection of a wide range of enveloped viruses including the four Dengue virus serotypes, influenza A virus, respiratory syncytial virus, tick-borne encephalitis virus, but not human adenovirus, a non-enveloped virus in vitro. This study establishes soluble recombinant α-DGN as a broad-band, natural compound candidate therapeutic against enveloped viruses.
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Affiliation(s)
- Maria Giulia Bigotti
- Bristol Heart Institute, Research Floor Level 7, Bristol Royal Infirmary, Bristol BS2 8HW, UK; School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK.
| | - Katja Klein
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK.
| | - Esther S Gan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Maria Anastasina
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland; Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Simon Andersson
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Pekka Katajisto
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland; Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, Helsinki, Finland; Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Solna, Sweden
| | - Maximilian Erdmann
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Andrew D Davidson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Sarah J Butcher
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland; Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ian Collinson
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Eng Eong Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore; Viral Research and Experimental Medicine Centre, SingHealth Duke-NUS Academic Medical Centre, 20 College Road, Singapore, 169856, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, #10-01, Singapore, 117549, Singapore
| | - Giuseppe Balistreri
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland; Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, Helsinki, Finland; Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Andrea Brancaccio
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK; Institute of Chemical Sciences and Technologies "Giulio Natta" (SCITEC)-CNR, Rome, Italy.
| | - Yohei Yamauchi
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK; Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences (D-CHAB), ETH Zurich, 8093, Zurich, Switzerland; Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
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6
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Thümmler L, Beckmann N, Sehl C, Soddemann M, Braß P, Bormann M, Brochhagen L, Elsner C, Hoertel N, Cougoule C, Ciesek S, Widera M, Dittmer U, Lindemann M, Horn PA, Witzke O, Kadow S, Kamler M, Gulbins E, Becker KA, Krawczyk A. Fluoxetine and Sertraline Potently Neutralize the Replication of Distinct SARS-CoV-2 Variants. Viruses 2024; 16:545. [PMID: 38675888 PMCID: PMC11053511 DOI: 10.3390/v16040545] [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: 02/15/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
The pandemic caused by SARS-CoV-2 is still a major health problem. Newly emerging variants and long-COVID-19 represent a challenge for the global health system. In particular, individuals in developing countries with insufficient health care need easily accessible, affordable and effective treatments of COVID-19. Previous studies have demonstrated the efficacy of functional inhibitors of acid sphingomyelinase against infections with various viruses, including early variants of SARS-CoV-2. This work investigated whether the acid sphingomyelinase inhibitors fluoxetine and sertraline, usually used as antidepressant molecules in clinical practice, can inhibit the replication of the former and recently emerged SARS-CoV-2 variants in vitro. Fluoxetine and sertraline potently inhibited the infection with pseudotyped virus-like particles and SARS-CoV-2 variants D614G, alpha, delta, omicron BA.1 and omicron BA.5. These results highlight fluoxetine and sertraline as priority candidates for large-scale phase 3 clinical trials at different stages of SARS-CoV-2 infections, either alone or in combination with other medications.
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Affiliation(s)
- Laura Thümmler
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Medicine Essen, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany; (L.T.); (P.B.); (M.B.); (L.B.); (O.W.)
- Institute for Transfusion Medicine, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany; (M.L.); (P.A.H.)
| | - Nadine Beckmann
- Institute of Molecular Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany (C.S.); (M.S.); (S.K.); (E.G.); (K.A.B.)
| | - Carolin Sehl
- Institute of Molecular Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany (C.S.); (M.S.); (S.K.); (E.G.); (K.A.B.)
| | - Matthias Soddemann
- Institute of Molecular Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany (C.S.); (M.S.); (S.K.); (E.G.); (K.A.B.)
| | - Peer Braß
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Medicine Essen, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany; (L.T.); (P.B.); (M.B.); (L.B.); (O.W.)
| | - Maren Bormann
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Medicine Essen, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany; (L.T.); (P.B.); (M.B.); (L.B.); (O.W.)
| | - Leonie Brochhagen
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Medicine Essen, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany; (L.T.); (P.B.); (M.B.); (L.B.); (O.W.)
| | - Carina Elsner
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany; (C.E.); (U.D.)
| | - Nicolas Hoertel
- Institute Psychiatry and Neuroscience de Paris, INSERM U1266, Paris Cité University, 75014 Paris, France;
- Psychiatry and Addiction Department Corentin-Celton Hospital (AP-HP), 92130 Paris, France
| | - Céline Cougoule
- Institute of Pharmacology and Structural Biology (IPBS), CNRS, University of Toulouse, UPS, 31000 Toulouse, France;
| | - Sandra Ciesek
- Institute of Medical Virology, University Hospital Frankfurt, 60590 Frankfurt am Main, Germany; (S.C.); (M.W.)
- Institute of Pharmaceutical Biology, Goethe-University, 60323 Frankfurt am Main, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch Translational Medicine and Pharmacology, 60311 Frankfurt am Main, Germany
| | - Marek Widera
- Institute of Medical Virology, University Hospital Frankfurt, 60590 Frankfurt am Main, Germany; (S.C.); (M.W.)
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany; (C.E.); (U.D.)
| | - Monika Lindemann
- Institute for Transfusion Medicine, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany; (M.L.); (P.A.H.)
| | - Peter A. Horn
- Institute for Transfusion Medicine, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany; (M.L.); (P.A.H.)
| | - Oliver Witzke
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Medicine Essen, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany; (L.T.); (P.B.); (M.B.); (L.B.); (O.W.)
| | - Stephanie Kadow
- Institute of Molecular Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany (C.S.); (M.S.); (S.K.); (E.G.); (K.A.B.)
| | - Markus Kamler
- Department of Thoracic and Cardiovascular Surgery, West German Heart Center, University Hospital Essen, 45147 Essen, Germany;
| | - Erich Gulbins
- Institute of Molecular Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany (C.S.); (M.S.); (S.K.); (E.G.); (K.A.B.)
| | - Katrin Anne Becker
- Institute of Molecular Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany (C.S.); (M.S.); (S.K.); (E.G.); (K.A.B.)
| | - Adalbert Krawczyk
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Medicine Essen, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany; (L.T.); (P.B.); (M.B.); (L.B.); (O.W.)
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany; (C.E.); (U.D.)
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7
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Zhang L, Kempf A, Nehlmeier I, Cossmann A, Richter A, Bdeir N, Graichen L, Moldenhauer AS, Dopfer-Jablonka A, Stankov MV, Simon-Loriere E, Schulz SR, Jäck HM, Čičin-Šain L, Behrens GMN, Drosten C, Hoffmann M, Pöhlmann S. SARS-CoV-2 BA.2.86 enters lung cells and evades neutralizing antibodies with high efficiency. Cell 2024; 187:596-608.e17. [PMID: 38194966 DOI: 10.1016/j.cell.2023.12.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/03/2023] [Accepted: 12/18/2023] [Indexed: 01/11/2024]
Abstract
BA.2.86, a recently identified descendant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2 sublineage, contains ∼35 mutations in the spike (S) protein and spreads in multiple countries. Here, we investigated whether the virus exhibits altered biological traits, focusing on S protein-driven viral entry. Employing pseudotyped particles, we show that BA.2.86, unlike other Omicron sublineages, enters Calu-3 lung cells with high efficiency and in a serine- but not cysteine-protease-dependent manner. Robust lung cell infection was confirmed with authentic BA.2.86, but the virus exhibited low specific infectivity. Further, BA.2.86 was highly resistant against all therapeutic antibodies tested, efficiently evading neutralization by antibodies induced by non-adapted vaccines. In contrast, BA.2.86 and the currently circulating EG.5.1 sublineage were appreciably neutralized by antibodies induced by the XBB.1.5-adapted vaccine. Collectively, BA.2.86 has regained a trait characteristic of early SARS-CoV-2 lineages, robust lung cell entry, and evades neutralizing antibodies. However, BA.2.86 exhibits low specific infectivity, which might limit transmissibility.
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Affiliation(s)
- Lu Zhang
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany
| | - Anne Cossmann
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Anja Richter
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Najat Bdeir
- Department of Viral Immunology, Helmholtz Zentrum für Infektionsforschung, 38124 Braunschweig, Germany
| | - Luise Graichen
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | | | - Alexandra Dopfer-Jablonka
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 30625 Hannover, Germany
| | - Metodi V Stankov
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Etienne Simon-Loriere
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, 75015 Paris, France; National Reference Center for Viruses of respiratory Infections, Institut Pasteur, 75015 Paris, France
| | - Sebastian R Schulz
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Luka Čičin-Šain
- Department of Viral Immunology, Helmholtz Zentrum für Infektionsforschung, 38124 Braunschweig, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 30625 Hannover, Germany; Center for Individualized Infection Medicine, a joint venture of HZI and MHH, 30625 Hannover, Germany
| | - Georg M N Behrens
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 30625 Hannover, Germany; Center for Individualized Infection Medicine, a joint venture of HZI and MHH, 30625 Hannover, Germany
| | - Christian Drosten
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany.
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany.
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8
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Acar DD, Witkowski W, Wejda M, Wei R, Desmet T, Schepens B, De Cae S, Sedeyn K, Eeckhaut H, Fijalkowska D, Roose K, Vanmarcke S, Poupon A, Jochmans D, Zhang X, Abdelnabi R, Foo CS, Weynand B, Reiter D, Callewaert N, Remaut H, Neyts J, Saelens X, Gerlo S, Vandekerckhove L. Integrating artificial intelligence-based epitope prediction in a SARS-CoV-2 antibody discovery pipeline: caution is warranted. EBioMedicine 2024; 100:104960. [PMID: 38232633 PMCID: PMC10803917 DOI: 10.1016/j.ebiom.2023.104960] [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: 05/01/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND SARS-CoV-2-neutralizing antibodies (nABs) showed great promise in the early phases of the COVID-19 pandemic. The emergence of resistant strains, however, quickly rendered the majority of clinically approved nABs ineffective. This underscored the imperative to develop nAB cocktails targeting non-overlapping epitopes. METHODS Undertaking a nAB discovery program, we employed a classical workflow, while integrating artificial intelligence (AI)-based prediction to select non-competing nABs very early in the pipeline. We identified and in vivo validated (in female Syrian hamsters) two highly potent nABs. FINDINGS Despite the promising results, in depth cryo-EM structural analysis demonstrated that the AI-based prediction employed with the intention to ensure non-overlapping epitopes was inaccurate. The two nABs in fact bound to the same receptor-binding epitope in a remarkably similar manner. INTERPRETATION Our findings indicate that, even in the Alphafold era, AI-based predictions of paratope-epitope interactions are rough and experimental validation of epitopes remains an essential cornerstone of a successful nAB lead selection. FUNDING Full list of funders is provided at the end of the manuscript.
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Affiliation(s)
- Delphine Diana Acar
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Wojciech Witkowski
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Magdalena Wejda
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Ruifang Wei
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Tim Desmet
- Department of Basic and Applied Medical Sciences, Ghent University, Ghent 9000, Belgium
| | - Bert Schepens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Sieglinde De Cae
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Koen Sedeyn
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Hannah Eeckhaut
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Daria Fijalkowska
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Kenny Roose
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Sandrine Vanmarcke
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | | | - Dirk Jochmans
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Xin Zhang
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Rana Abdelnabi
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Caroline S Foo
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Birgit Weynand
- Department of Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven, Leuven 3000, Belgium
| | - Dirk Reiter
- Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | - Nico Callewaert
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Han Remaut
- Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels 1050, Belgium; VIB-VUB Center for Structural Biology, VIB, Brussels 1050, Belgium
| | - Johan Neyts
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Sarah Gerlo
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent 9000, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium.
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9
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Li R, Chang Z, Liu H, Wang Y, Li M, Chen Y, Fan L, Wang S, Sun X, Liu S, Cheng A, Ding P, Zhang G. Double-layered N-S1 protein nanoparticle immunization elicits robust cellular immune and broad antibody responses against SARS-CoV-2. J Nanobiotechnology 2024; 22:44. [PMID: 38291444 PMCID: PMC10825999 DOI: 10.1186/s12951-024-02293-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/02/2024] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND The COVID-19 pandemic is a persistent global threat to public health. As for the emerging variants of SARS-CoV-2, it is necessary to develop vaccines that can induce broader immune responses, particularly vaccines with weak cellular immunity. METHODS In this study, we generated a double-layered N-S1 protein nanoparticle (N-S1 PNp) that was formed by desolvating N protein into a protein nanoparticle as the core and crosslinking S1 protein onto the core surface against SARS-CoV-2. RESULTS Vaccination with N-S1 PNp elicited robust humoral and vigorous cellular immune responses specific to SARS-CoV-2 in mice. Compared to soluble protein groups, the N-S1 PNp induced a higher level of humoral response, as evidenced by the ability of S1-specific antibodies to block hACE2 receptor binding and neutralize pseudovirus. Critically, N-S1 PNp induced Th1-biased, long-lasting, and cross-neutralizing antibodies, which neutralized the variants of SARS-CoV-2 with minimal loss of activity. N-S1 PNp induced strong responses of CD4+ and CD8+ T cells, mDCs, Tfh cells, and GCs B cells in spleens. CONCLUSIONS These results demonstrate that N-S1 PNp vaccination is a practical approach for promoting protection, which has the potential to counteract the waning immune responses against SARS-CoV-2 variants and confer broad efficacy against future new variants. This study provides a new idea for the design of next-generation SARS-CoV-2 vaccines based on the B and T cells response coordination.
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Affiliation(s)
- Ruiqi Li
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
- School of Advanced Agricultural Sciences , Peking University, Beijing, 100080, China
- Longhu Laboratory, Zhengzhou, 450046, China
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Zejie Chang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
- College of Animal Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Hongliang Liu
- School of Life Sciences , Zhengzhou University, Zhengzhou, 450001, China
| | - Yanan Wang
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
- College of Animal Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Minghui Li
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
- College of Animal Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yilan Chen
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Lu Fan
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Siqiao Wang
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Xueke Sun
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
- College of Animal Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Siyuan Liu
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
- College of Animal Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Anchun Cheng
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Peiyang Ding
- School of Life Sciences , Zhengzhou University, Zhengzhou, 450001, China.
| | - Gaiping Zhang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
- School of Advanced Agricultural Sciences , Peking University, Beijing, 100080, China.
- Longhu Laboratory, Zhengzhou, 450046, China.
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
- College of Animal Medicine, Henan Agricultural University, Zhengzhou, 450046, China.
- School of Life Sciences , Zhengzhou University, Zhengzhou, 450001, China.
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10
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Schoefbaenker M, Neddermeyer R, Guenther T, Mueller MM, Romberg ML, Classen N, Hennies MT, Hrincius ER, Ludwig S, Kuehn JE, Lorentzen EU. Surrogate Virus Neutralisation Test Based on Nanoluciferase-Tagged Antigens to Quantify Inhibitory Antibodies against SARS-CoV-2 and Characterise Omicron-Specific Reactivity in a Vaccination Cohort. Vaccines (Basel) 2023; 11:1832. [PMID: 38140236 PMCID: PMC10748151 DOI: 10.3390/vaccines11121832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Virus-specific antibodies are crucial for protective immunity against SARS-CoV-2. Assessing functional antibodies through conventional or pseudotyped virus neutralisation tests (pVNT) requires high biosafety levels. Alternatively, the virus-free surrogate virus neutralisation test (sVNT) quantifies antibodies interfering with spike binding to angiotensin-converting enzyme 2. We evaluated secreted nanoluciferase-tagged spike protein fragments as diagnostic antigens in the sVNT in a vaccination cohort. Initially, spike fragments were tested in a capture enzyme immunoassay (EIA), identifying the receptor binding domain (RBD) as the optimal diagnostic antigen. The sensitivity of the in-house sVNT applying the nanoluciferase-labelled RBD equalled or surpassed that of a commercial sVNT (cPass, GenScript Diagnostics) and an in-house pVNT four weeks after the first vaccination (98% vs. 94% and 72%, respectively), reaching 100% in all assays four weeks after the second and third vaccinations. When testing serum reactivity with Omicron BA.1 spike, the sVNT and pVNT displayed superior discrimination between wild-type- and variant-specific serum reactivity compared to a capture EIA. This was most pronounced after the first and second vaccinations, with the third vaccination resulting in robust, cross-reactive BA.1 construct detection. In conclusion, utilising nanoluciferase-labelled antigens permits the quantification of SARS-CoV-2-specific inhibitory antibodies. Designed as flexible modular systems, the assays can be readily adjusted for monitoring vaccine efficacy.
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Affiliation(s)
- Michael Schoefbaenker
- Institute of Virology, Department of Molecular Virology, University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany; (M.S.); (E.R.H.); (S.L.)
| | - Rieke Neddermeyer
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
| | - Theresa Guenther
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
| | - Marlin M. Mueller
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
| | - Marie-Luise Romberg
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
| | - Nica Classen
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
- Institute of Pharmaceutical Biology and Phytochemistry, University of Muenster, Corrensstr. 48, D-48149 Muenster, Germany
| | - Marc T. Hennies
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
| | - Eike R. Hrincius
- Institute of Virology, Department of Molecular Virology, University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany; (M.S.); (E.R.H.); (S.L.)
| | - Stephan Ludwig
- Institute of Virology, Department of Molecular Virology, University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany; (M.S.); (E.R.H.); (S.L.)
| | - Joachim E. Kuehn
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
| | - Eva U. Lorentzen
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
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11
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Amalfi S, Plastine MDP, López MG, Gravisaco MJ, Taboga O, Alfonso V. P26 enhances baculovirus gene delivery by modulating the mammalian antiviral response. Appl Microbiol Biotechnol 2023; 107:6277-6286. [PMID: 37578557 DOI: 10.1007/s00253-023-12703-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/14/2023] [Accepted: 07/22/2023] [Indexed: 08/15/2023]
Abstract
Poxins are poxviral proteins that act by degrading 2´3´-cGAMP, a key molecule of cGAS-STING axis that drives and amplifies the antiviral response. Previous works have described some poxin homologous among lepidopteran and baculoviral genes. In particular, P26, a poxin homologous from AcMNPV retains the 2´3´-cGAMP degradation activity in vitro. In this work, we demonstrated that the antiviral activity triggered by baculovirus was disrupted by the transient expression of P26 in murine and human cell lines, and the effect of this action is not only on IFN-β production but also on the induction of IFN-λ. Besides, we proved P26 functionality in a stable-transformed cell line where the protein was constitutively expressed, preventing the production of IFN-β induced by baculovirus and resulting in an improvement in the transduction efficiency by the attenuation of the antiviral activity. Finally, we incorporated P26 into budded virions by capsid display or passive incorporation, and the results showed that both strategies resulted in an improvement of 3-17 times in the efficiency of transgene expression in murine fibroblasts. Our results suggest that the incorporation of P26 to budded baculoviral vectors is a very promising tool to modulate negatively the innate antiviral cellular response and to improve the efficiency of gene delivery in mammalian cells. KEY POINTS: • P26 affects baculovirus-induced IFN-β and IFN-λ production in mammalian cells. • Murine fibroblasts expressing P26 are more susceptible to transduction by baculovirus. • Incorporation of P26 into the virion improves gene delivery efficiency of baculovirus.
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Affiliation(s)
- Sabrina Amalfi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De los Reseros y N. Repetto s/n, B1686IGC, Hurlingham, Buenos Aires, Argentina
- Instituto de Biotecnología, Universidad Nacional de Hurlingham, Av. Vergara 2222, Villa Tesei, B1688GEZ, Hurlingham, Buenos Aires, Argentina
| | - María Del Pilar Plastine
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De los Reseros y N. Repetto s/n, B1686IGC, Hurlingham, Buenos Aires, Argentina
| | - María Gabriela López
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De los Reseros y N. Repetto s/n, B1686IGC, Hurlingham, Buenos Aires, Argentina
| | - María José Gravisaco
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De los Reseros y N. Repetto s/n, B1686IGC, Hurlingham, Buenos Aires, Argentina
| | - Oscar Taboga
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De los Reseros y N. Repetto s/n, B1686IGC, Hurlingham, Buenos Aires, Argentina.
| | - Victoria Alfonso
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De los Reseros y N. Repetto s/n, B1686IGC, Hurlingham, Buenos Aires, Argentina
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12
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Gilbertson B, Subbarao K. What Have We Learned by Resurrecting the 1918 Influenza Virus? Annu Rev Virol 2023; 10:25-47. [PMID: 37774132 DOI: 10.1146/annurev-virology-111821-104408] [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: 10/01/2023]
Abstract
The 1918 Spanish influenza pandemic was one of the deadliest infectious disease events in recorded history, resulting in approximately 50-100 million deaths worldwide. The origins of the 1918 virus and the molecular basis for its exceptional virulence remained a mystery for much of the 20th century because the pandemic predated virologic techniques to isolate, passage, and store influenza viruses. In the late 1990s, overlapping fragments of influenza viral RNA preserved in the tissues of several 1918 victims were amplified and sequenced. The use of influenza reverse genetics then permitted scientists to reconstruct the 1918 virus entirely from cloned complementary DNA, leading to new insights into the origin of the virus and its pathogenicity. Here, we discuss some of the advances made by resurrection of the 1918 virus, including the rise of innovative molecular research, which is a topic in the dual use debate.
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Affiliation(s)
- Brad Gilbertson
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia;
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13
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Thompson D, Cismaru CV, Rougier JS, Schwemmle M, Zimmer G. The M2 proteins of bat influenza A viruses reveal atypical features compared to conventional M2 proteins. J Virol 2023; 97:e0038823. [PMID: 37540019 PMCID: PMC10506471 DOI: 10.1128/jvi.00388-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 06/14/2023] [Indexed: 08/05/2023] Open
Abstract
The influenza A virus (IAV) M2 protein has proton channel activity, which plays a role in virus uncoating and may help to preserve the metastable conformation of the IAV hemagglutinin (HA). In contrast to the highly conserved M2 proteins of conventional IAV, the primary sequences of bat IAV H17N10 and H18N11 M2 proteins show remarkable divergence, suggesting that these proteins may differ in their biological function. We, therefore, assessed the proton channel activity of bat IAV M2 proteins and investigated its role in virus replication. Here, we show that the M2 proteins of bat IAV did not fully protect acid-sensitive HA of classical IAV from low pH-induced conformational change, indicating low proton channel activity. Interestingly, the N31S substitution not only rendered bat IAV M2 proteins sensitive to inhibition by amantadine but also preserved the metastable conformation of acid-sensitive HA to a greater extent. In contrast, the acid-stable HA of H18N11 did not rely on such support by M2 protein. When mutant M2(N31S) protein was expressed in the context of chimeric H18N11/H5N1(6:2) encoding HA and NA of avian IAV H5N1, amantadine significantly inhibited virus entry, suggesting that ion channel activity supported virus uncoating. Finally, the cytoplasmic domain of the H18N11 M2 protein mediated rapid internalization of the protein from the plasma membrane leading to low-level expression at the cell surface. However, cell surface levels of H18N11 M2 protein were significantly enhanced in cells infected with the chimeric H18N11/H5N1(6:2) virus. The potential role of the N1 sialidase in arresting M2 internalization is discussed. IMPORTANCE Bat IAV M2 proteins not only differ from the homologous proteins of classical IAV by their divergent primary sequence but are also unable to preserve the metastable conformation of acid-sensitive HA, indicating low proton channel activity. This unusual feature may help to avoid M2-mediated cytotoxic effects and inflammation in bats infected with H17N10 or H18N11. Unlike classical M2 proteins, bat IAV M2 proteins with the N31S substitution mediated increased protection of HA from acid-induced conformational change. This remarkable gain of function may help to understand how single point mutations can modulate proton channel activity. In addition, the cytoplasmic domain was found to be responsible for the low cell surface expression level of bat IAV M2 proteins. Given that the M2 cytoplasmic domain of conventional IAV is well known to participate in virus assembly at the plasma membrane, this atypical feature might have consequences for bat IAV budding and egress.
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Affiliation(s)
- Danielle Thompson
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Christiana Victoria Cismaru
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | | | - Martin Schwemmle
- Institute of Virology, Medical Center – University of Freiburg, Freiburg im Breisgau, Germany
| | - Gert Zimmer
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
- Department of Pathology and Infectious Diseases, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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14
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Muik A, Lui BG, Quandt J, Diao H, Fu Y, Bacher M, Gordon J, Toker A, Grosser J, Ozhelvaci O, Grikscheit K, Hoehl S, Kohmer N, Lustig Y, Regev-Yochay G, Ciesek S, Beguir K, Poran A, Vogler I, Türeci Ö, Sahin U. Progressive loss of conserved spike protein neutralizing antibody sites in Omicron sublineages is balanced by preserved T cell immunity. Cell Rep 2023; 42:112888. [PMID: 37527039 DOI: 10.1016/j.celrep.2023.112888] [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: 03/17/2023] [Revised: 03/27/2023] [Accepted: 07/13/2023] [Indexed: 08/03/2023] Open
Abstract
Evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has led to the emergence of sublineages with different patterns of neutralizing antibody evasion. We report that Omicron BA.4/BA.5 breakthrough infection of individuals immunized with SARS-CoV-2 wild-type-strain-based mRNA vaccines results in a boost of Omicron BA.4.6, BF.7, BQ.1.1, and BA.2.75 neutralization but does not efficiently boost BA.2.75.2, XBB, or XBB.1.5 neutralization. In silico analyses showed that the Omicron spike glycoprotein lost most neutralizing B cell epitopes, especially in sublineages BA.2.75.2, XBB, and XBB.1.5. In contrast, T cell epitopes are conserved across variants including XBB.1.5. T cell responses of mRNA-vaccinated, SARS-CoV-2-naive individuals against the wild-type strain, Omicron BA.1, and BA.4/BA.5 were comparable, suggesting that T cell immunity against recent sublineages including XBB.1.5 may remain largely unaffected. While some Omicron sublineages effectively evade B cell immunity, spike-protein-specific T cell immunity, due to the nature of polymorphic cell-mediated immune responses, may continue to contribute to prevention/limitation of severe COVID-19 manifestation.
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Affiliation(s)
| | | | | | - Huitian Diao
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA
| | - Yunguan Fu
- InstaDeep, Ltd., 5 Merchant Square, London W2 1AY, UK
| | - Maren Bacher
- BioNTech, An der Goldgrube 12, 55131 Mainz, Germany
| | | | - Aras Toker
- BioNTech, An der Goldgrube 12, 55131 Mainz, Germany
| | | | | | - Katharina Grikscheit
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Sebastian Hoehl
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Niko Kohmer
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Yaniv Lustig
- Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel; Central Virology Laboratory, Public Health Services, Ministry of Health, Tel-Hashomer, Ramat Gan, Israel
| | - Gili Regev-Yochay
- Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel; SPRI-Sheba Pandemic Preparedness Research Institute, Sheba Medical Center Tel Hashomer, Ramat Gan, Israel
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; DZIF - German Centre for Infection Research, External Partner Site, 60596 Frankfurt am Main, Germany
| | - Karim Beguir
- InstaDeep, Ltd., 5 Merchant Square, London W2 1AY, UK
| | - Asaf Poran
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA
| | | | - Özlem Türeci
- BioNTech, An der Goldgrube 12, 55131 Mainz, Germany; HI-TRON - Helmholtz Institute for Translational Oncology Mainz by DKFZ, Obere Zahlbacherstr. 63, 55131 Mainz, Germany
| | - Ugur Sahin
- BioNTech, An der Goldgrube 12, 55131 Mainz, Germany; TRON gGmbH - Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Freiligrathstraße 12, 55131 Mainz, Germany.
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15
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Gargantilla M, Francés C, Adhav A, Forcada-Nadal A, Martínez-Gualda B, Martí-Marí O, López-Redondo ML, Melero R, Marco-Marín C, Gougeard N, Espinosa C, Rubio-del-Campo A, Ruiz-Partida R, Hernández-Sierra MD, Villamayor-Belinchón L, Bravo J, Llacer JL, Marina A, Rubio V, San-Félix A, Geller R, Pérez-Pérez MJ. C-2 Thiophenyl Tryptophan Trimers Inhibit Cellular Entry of SARS-CoV-2 through Interaction with the Viral Spike (S) Protein. J Med Chem 2023; 66:10432-10457. [PMID: 37471688 PMCID: PMC10424185 DOI: 10.1021/acs.jmedchem.3c00576] [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: 03/31/2023] [Indexed: 07/22/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19, by infecting cells via the interaction of its spike protein (S) with the primary cell receptor angiotensin-converting enzyme (ACE2). To search for inhibitors of this key step in viral infection, we screened an in-house library of multivalent tryptophan derivatives. Using VSV-S pseudoparticles, we identified compound 2 as a potent entry inhibitor lacking cellular toxicity. Chemical optimization of 2 rendered compounds 63 and 65, which also potently inhibited genuine SARS-CoV-2 cell entry. Thermofluor and microscale thermophoresis studies revealed their binding to S and to its isolated receptor binding domain (RBD), interfering with the interaction with ACE2. High-resolution cryoelectron microscopy structure of S, free or bound to 2, shed light on cell entry inhibition mechanisms by these compounds. Overall, this work identifies and characterizes a new class of SARS-CoV-2 entry inhibitors with clear potential for preventing and/or fighting COVID-19.
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Affiliation(s)
- Marta Gargantilla
- Instituto de Química
Médica (IQM, CSIC), c/Juan de la Cierva 3, Madrid 28006, Spain
| | - Clara Francés
- Institute for Integrative Systems Biology (I2SysBio), UV-CSIC, c/Catedrático Agustin Escardino,
9, Paterna 46980, Valencia, Spain
| | - Anmol Adhav
- Instituto de Biomedicina de Valencia (IBV, CSIC), c/Jaime Roig 11, Valencia 46010, Spain
| | - Alicia Forcada-Nadal
- Instituto de Biomedicina de Valencia (IBV, CSIC), c/Jaime Roig 11, Valencia 46010, Spain
- Group 739, Centro de Investigación
Biomédica en Red en Enfermedades Raras (CIBERER-ISCIII), Madrid 28049, Spain
| | | | - Olaia Martí-Marí
- Instituto de Química
Médica (IQM, CSIC), c/Juan de la Cierva 3, Madrid 28006, Spain
| | | | - Roberto Melero
- Centro
Nacional de Biotecnología (CNB, CSIC), c/Darwin 3, Madrid 28049, Spain
| | - Clara Marco-Marín
- Instituto de Biomedicina de Valencia (IBV, CSIC), c/Jaime Roig 11, Valencia 46010, Spain
- Group 739, Centro de Investigación
Biomédica en Red en Enfermedades Raras (CIBERER-ISCIII), Madrid 28049, Spain
| | - Nadine Gougeard
- Instituto de Biomedicina de Valencia (IBV, CSIC), c/Jaime Roig 11, Valencia 46010, Spain
- Group 739, Centro de Investigación
Biomédica en Red en Enfermedades Raras (CIBERER-ISCIII), Madrid 28049, Spain
| | - Carolina Espinosa
- Instituto de Biomedicina de Valencia (IBV, CSIC), c/Jaime Roig 11, Valencia 46010, Spain
| | | | - Rafael Ruiz-Partida
- Instituto de Biomedicina de Valencia (IBV, CSIC), c/Jaime Roig 11, Valencia 46010, Spain
| | | | | | - Jerónimo Bravo
- Instituto de Biomedicina de Valencia (IBV, CSIC), c/Jaime Roig 11, Valencia 46010, Spain
| | - José-Luis Llacer
- Instituto de Biomedicina de Valencia (IBV, CSIC), c/Jaime Roig 11, Valencia 46010, Spain
- Group 739, Centro de Investigación
Biomédica en Red en Enfermedades Raras (CIBERER-ISCIII), Madrid 28049, Spain
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV, CSIC), c/Jaime Roig 11, Valencia 46010, Spain
- Group 739, Centro de Investigación
Biomédica en Red en Enfermedades Raras (CIBERER-ISCIII), Madrid 28049, Spain
| | - Vicente Rubio
- Instituto de Biomedicina de Valencia (IBV, CSIC), c/Jaime Roig 11, Valencia 46010, Spain
- Group 739, Centro de Investigación
Biomédica en Red en Enfermedades Raras (CIBERER-ISCIII), Madrid 28049, Spain
| | - Ana San-Félix
- Instituto de Química
Médica (IQM, CSIC), c/Juan de la Cierva 3, Madrid 28006, Spain
| | - Ron Geller
- Institute for Integrative Systems Biology (I2SysBio), UV-CSIC, c/Catedrático Agustin Escardino,
9, Paterna 46980, Valencia, Spain
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16
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Bäuerl C, Zulaica J, Rusu L, Moreno AR, Pérez-Cano FJ, Lerin C, Mena-Tudela D, Aguilar-Camprubí L, Parra-Llorca A, Martínez-Costa C, Geller R, Collado MC. Assessment of SARS-CoV-2 neutralizing antibody titers in breastmilk from convalescent and vaccinated mothers. iScience 2023; 26:106802. [PMID: 37197591 PMCID: PMC10158041 DOI: 10.1016/j.isci.2023.106802] [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: 02/16/2023] [Revised: 03/29/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Breastmilk contains antibodies that could protect breastfed infants from infections. In this work, we examined if antibodies in breastmilk could neutralize SARS-CoV-2 in 84 breastmilk samples from women that were either vaccinated (Comirnaty, mRNA-1273, or ChAdOx1), infected with SARS-CoV-2, or both infected and vaccinated. The neutralization capacity of these sera was tested using pseudotyped vesicular stomatitis virus carrying either the Wuhan-Hu-1, Delta, or BA.1 Omicron spike proteins. We found that natural infection resulted in higher neutralizing titers and that neutralization correlated positively with levels of immunoglobulin A in breastmilk. In addition, significant differences in the capacity to produce neutralizing antibodies were observed between both mRNA-based vaccines and the adenovirus-vectored ChAdOx1 COVID-19 vaccine. Overall, our results indicate that breastmilk from naturally infected women or those vaccinated with mRNA-based vaccines contains SARS-CoV-2 neutralizing antibodies that could potentially provide protection to breastfed infants from infection.
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Affiliation(s)
- Christine Bäuerl
- Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), 46980 Paterna, Valencia, Spain
| | - Joao Zulaica
- Institute for Integrative Systems Biology (ISysBio), University of Valencia-CSIC, 46980 Paterna, Valencia, Spain
| | - Luciana Rusu
- Institute for Integrative Systems Biology (ISysBio), University of Valencia-CSIC, 46980 Paterna, Valencia, Spain
| | - Alicia Rodríguez Moreno
- Institute for Integrative Systems Biology (ISysBio), University of Valencia-CSIC, 46980 Paterna, Valencia, Spain
| | - Francisco J. Pérez-Cano
- Physiology Section, Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Science and Institute of Research in Nutrition and Food Safety (INSA), University of Barcelona (UB), 08028 Barcelona, Spain
| | - Carles Lerin
- Endocrinology department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Desirée Mena-Tudela
- Department of Nursing, Nursing Research Group, Universitat Jaume I, Castellón, Spain
| | | | - Anna Parra-Llorca
- Health Research Institute La Fe, Neonatal Research Group, Spain and University and Polytechnic Hospital La Fe, Division of Neonatology, 46026 Valencia, Spain
| | - Cecilia Martínez-Costa
- Department of Pediatrics, Hospital Clínico Universitario, University of Valencia, Spain. Nutrition Research Group of INCLIVA, 46010 Valencia, Spain
| | - Ron Geller
- Institute for Integrative Systems Biology (ISysBio), University of Valencia-CSIC, 46980 Paterna, Valencia, Spain
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), 46980 Paterna, Valencia, Spain
| | - MilkCORONA study team
- Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), 46980 Paterna, Valencia, Spain
- Institute for Integrative Systems Biology (ISysBio), University of Valencia-CSIC, 46980 Paterna, Valencia, Spain
- Physiology Section, Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Science and Institute of Research in Nutrition and Food Safety (INSA), University of Barcelona (UB), 08028 Barcelona, Spain
- Endocrinology department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Nursing, Nursing Research Group, Universitat Jaume I, Castellón, Spain
- LactApp Women Health, Barcelona, Spain
- Health Research Institute La Fe, Neonatal Research Group, Spain and University and Polytechnic Hospital La Fe, Division of Neonatology, 46026 Valencia, Spain
- Department of Pediatrics, Hospital Clínico Universitario, University of Valencia, Spain. Nutrition Research Group of INCLIVA, 46010 Valencia, Spain
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17
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Hoffmann M, Wong LYR, Arora P, Zhang L, Rocha C, Odle A, Nehlmeier I, Kempf A, Richter A, Halwe NJ, Schön J, Ulrich L, Hoffmann D, Beer M, Drosten C, Perlman S, Pöhlmann S. Omicron subvariant BA.5 efficiently infects lung cells. Nat Commun 2023; 14:3500. [PMID: 37311762 DOI: 10.1038/s41467-023-39147-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 05/26/2023] [Indexed: 06/15/2023] Open
Abstract
The SARS-CoV-2 Omicron subvariants BA.1 and BA.2 exhibit reduced lung cell infection relative to previously circulating SARS-CoV-2 variants, which may account for their reduced pathogenicity. However, it is unclear whether lung cell infection by BA.5, which displaced these variants, remains attenuated. Here, we show that the spike (S) protein of BA.5 exhibits increased cleavage at the S1/S2 site and drives cell-cell fusion and lung cell entry with higher efficiency than its counterparts from BA.1 and BA.2. Increased lung cell entry depends on mutation H69Δ/V70Δ and is associated with efficient replication of BA.5 in cultured lung cells. Further, BA.5 replicates in the lungs of female Balb/c mice and the nasal cavity of female ferrets with much higher efficiency than BA.1. These results suggest that BA.5 has acquired the ability to efficiently infect lung cells, a prerequisite for causing severe disease, suggesting that evolution of Omicron subvariants can result in partial loss of attenuation.
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Affiliation(s)
- Markus Hoffmann
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany.
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany.
| | - Lok-Yin Roy Wong
- Departments of Microbiology and Immunology, BSB 3-712, University of Iowa, Iowa City, IA, USA
| | - Prerna Arora
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Lu Zhang
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Cheila Rocha
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Abby Odle
- Departments of Microbiology and Immunology, BSB 3-712, University of Iowa, Iowa City, IA, USA
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Anja Richter
- Institute of Virology, Charité - Universitätsmedizin Berlin, Campus Charité Mitte, Berlin, Germany
| | - Nico Joel Halwe
- Institut für Virusdiagnostik (IVD), Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Jacob Schön
- Institut für Virusdiagnostik (IVD), Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Lorenz Ulrich
- Institut für Virusdiagnostik (IVD), Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Donata Hoffmann
- Institut für Virusdiagnostik (IVD), Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Martin Beer
- Institut für Virusdiagnostik (IVD), Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, Campus Charité Mitte, Berlin, Germany
| | - Stanley Perlman
- Departments of Microbiology and Immunology, BSB 3-712, University of Iowa, Iowa City, IA, USA
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany.
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany.
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18
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Ha DP, Shin WJ, Hernandez JC, Neamati N, Dubeau L, Machida K, Lee AS. GRP78 Inhibitor YUM70 Suppresses SARS-CoV-2 Viral Entry, Spike Protein Production and Ameliorates Lung Damage. Viruses 2023; 15:v15051118. [PMID: 37243204 DOI: 10.3390/v15051118] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID-19 pandemic, has given rise to many new variants with increased transmissibility and the ability to evade vaccine protection. The 78-kDa glucose-regulated protein (GRP78) is a major endoplasmic reticulum (ER) chaperone that has been recently implicated as an essential host factor for SARS-CoV-2 entry and infection. In this study, we investigated the efficacy of YUM70, a small molecule inhibitor of GRP78, to block SARS-CoV-2 viral entry and infection in vitro and in vivo. Using human lung epithelial cells and pseudoviral particles carrying spike proteins from different SARS-CoV-2 variants, we found that YUM70 was equally effective at blocking viral entry mediated by original and variant spike proteins. Furthermore, YUM70 reduced SARS-CoV-2 infection without impacting cell viability in vitro and suppressed viral protein production following SARS-CoV-2 infection. Additionally, YUM70 rescued the cell viability of multi-cellular human lung and liver 3D organoids transfected with a SARS-CoV-2 replicon. Importantly, YUM70 treatment ameliorated lung damage in transgenic mice infected with SARS-CoV-2, which correlated with reduced weight loss and longer survival. Thus, GRP78 inhibition may be a promising approach to augment existing therapies to block SARS-CoV-2, its variants, and other viruses that utilize GRP78 for entry and infection.
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Affiliation(s)
- Dat P Ha
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Woo-Jin Shin
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL 34987, USA
| | - Juan Carlos Hernandez
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy and Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Louis Dubeau
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Keigo Machida
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Amy S Lee
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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19
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Beguir K, Skwark MJ, Fu Y, Pierrot T, Carranza NL, Laterre A, Kadri I, Korched A, Lowegard AU, Lui BG, Sänger B, Liu Y, Poran A, Muik A, Şahin U. Early computational detection of potential high-risk SARS-CoV-2 variants. Comput Biol Med 2023; 155:106618. [PMID: 36774893 PMCID: PMC9892295 DOI: 10.1016/j.compbiomed.2023.106618] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/12/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023]
Abstract
The ongoing COVID-19 pandemic is leading to the discovery of hundreds of novel SARS-CoV-2 variants daily. While most variants do not impact the course of the pandemic, some variants pose an increased risk when the acquired mutations allow better evasion of antibody neutralisation or increased transmissibility. Early detection of such high-risk variants (HRVs) is paramount for the proper management of the pandemic. However, experimental assays to determine immune evasion and transmissibility characteristics of new variants are resource-intensive and time-consuming, potentially leading to delays in appropriate responses by decision makers. Presented herein is a novel in silico approach combining spike (S) protein structure modelling and large protein transformer language models on S protein sequences to accurately rank SARS-CoV-2 variants for immune escape and fitness potential. Both metrics were experimentally validated using in vitro pseudovirus-based neutralisation test and binding assays and were subsequently combined to explore the changing landscape of the pandemic and to create an automated Early Warning System (EWS) capable of evaluating new variants in minutes and risk-monitoring variant lineages in near real-time. The system accurately pinpoints the putatively dangerous variants by selecting on average less than 0.3% of the novel variants each week. The EWS flagged all 16 variants designated by the World Health Organization (WHO) as variants of interest (VOIs) if applicable or variants of concern (VOCs) otherwise with an average lead time of more than one and a half months ahead of their designation as such.
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Affiliation(s)
- Karim Beguir
- InstaDeep Ltd, 5 Merchant Square, London, W2 1AY, UK.
| | | | - Yunguan Fu
- InstaDeep Ltd, 5 Merchant Square, London, W2 1AY, UK
| | | | | | | | | | - Abir Korched
- InstaDeep Ltd, 5 Merchant Square, London, W2 1AY, UK
| | | | | | - Bianca Sänger
- BioNTech SE, An der Goldgrube 12, 55131, Mainz, Germany
| | - Yunpeng Liu
- BioNTech US, 40 Erie Street, Cambridge, MA, 02139, USA
| | - Asaf Poran
- BioNTech US, 40 Erie Street, Cambridge, MA, 02139, USA
| | | | - Uğur Şahin
- BioNTech SE, An der Goldgrube 12, 55131, Mainz, Germany.
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20
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LRP6 Is a Functional Receptor for Attenuated Canine Distemper Virus. mBio 2023; 14:e0311422. [PMID: 36645301 PMCID: PMC9973313 DOI: 10.1128/mbio.03114-22] [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] [Indexed: 01/17/2023] Open
Abstract
Wild-type canine distemper virus (CDV) is an important pathogen of dogs as well as wildlife that can infect immune and epithelial cells through two known receptors: the signaling lymphocytic activation molecule (SLAM) and nectin-4, respectively. Conversely, the ferret and egg-adapted CDV-Onderstepoort strain (CDV-OP) is employed as an effective vaccine for dogs. CDV-OP also exhibits promising oncolytic properties, such as its abilities to infect and kill multiple cancer cells in vitro. Interestingly, several cancer cells do not express SLAM or nectin-4, suggesting the presence of a yet unknown entry factor for CDV-OP. By conducting a genome-wide CRISPR/Cas9 knockout (KO) screen in CDV-OP-susceptible canine mammary carcinoma P114 cells, which neither express SLAM nor nectin-4, we identified low-density lipoprotein receptor-related protein 6 (LRP6) as a host factor that promotes CDV-OP infectivity. Whereas the genetic ablation of LRP6 rendered cells resistant to infection, ectopic expression in resistant LRP6KO cells restored susceptibility. Furthermore, multiple functional studies revealed that (i) the overexpression of LRP6 leads to increased cell-cell fusion, (ii) a soluble construct of the viral receptor-binding protein (solHOP) interacts with a soluble form of LRP6 (solLRP6), (iii) an H-OP point mutant that prevents interaction with solLRP6 abrogates cell entry in multiple cell lines once transferred into recombinant viral particles, and (iv) vesicular stomatitis virus (VSV) pseudotyped with CDV-OP envelope glycoproteins loses its infectivity in LRP6KO cells. Collectively, our study identified LRP6 as the long sought-after cell entry receptor of CDV-OP in multiple cell lines, which set the molecular bases to refine our understanding of viral-cell adaptation and to further investigate its oncolytic properties. IMPORTANCE Oncolytic viruses (OV) have gathered increasing interest in recent years as an alternative option to treat cancers. The Onderstepoort strain of canine distemper virus (CDV-OP), an enveloped RNA virus belonging to the genus Morbillivirus, is employed as a safe and efficient vaccine for dogs against distemper disease. Importantly, although CDV-OP can infect and kill multiple cancer cell lines, the basic mechanisms of entry remain to be elucidated, as most of those transformed cells do not express natural receptors (i.e., SLAM and nectin-4). In this study, using a genome-wide CRISPR/Cas9 knockout screen, we describe the discovery of LRP6 as a novel functional entry receptor for CDV-OP in various cancer cell lines and thereby uncover a basic mechanism of cell culture adaptation. Since LRP6 is upregulated in various cancer types, our data provide important insights in order to further investigate the oncolytic properties of CDV-OP.
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Monitoring and immunogenicity of SARS-CoV-2 vaccination of laboratory rhesus monkeys (Macaca mulatta). Sci Rep 2023; 13:3274. [PMID: 36841887 PMCID: PMC9958316 DOI: 10.1038/s41598-023-30473-7] [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: 11/24/2022] [Accepted: 02/23/2023] [Indexed: 02/27/2023] Open
Abstract
The availability of effective vaccines and a high vaccination rate allowed the recent mitigation, or even withdrawal, of many protective measures for containing the SARS CoV-2 pandemic. At the same time, new and highly mutated variants of the virus are found to have significantly higher transmissibility and reduced vaccine efficacy, thus causing high infection rates during the third year of the pandemic. The combination of reduced measures and increased infectivity poses a particular risk for unvaccinated individuals, including animals susceptible to the virus. Among the latter, non-human primates (NHPs) are particularly vulnerable. They serve as important models in various fields of biomedical research and because of their cognitive capabilities, they receive particular attention in animal welfare regulations around the world. Yet, although they played an extraordinarily important role for developing and testing vaccines against SARS-CoV-2, the protection of captive rhesus monkeys against Covid-19 has rarely been discussed. We here report upon twofold mRNA vaccination of a cohort of 19 elderly rhesus monkeys (Macaca mulatta) against infection by SARS-CoV-2. All animals were closely monitored on possible side effects of vaccination, and were tested for neutralising antibodies against the virus. The data show that vaccination of rhesus monkeys is a safe and reliable measure to protect these animals against SARS-CoV-2.
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22
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Despic V, Jaffrey SR. mRNA ageing shapes the Cap2 methylome in mammalian mRNA. Nature 2023; 614:358-366. [PMID: 36725932 PMCID: PMC9891201 DOI: 10.1038/s41586-022-05668-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 12/16/2022] [Indexed: 02/03/2023]
Abstract
The mRNA cap structure is a major site of dynamic mRNA methylation. mRNA caps exist in either the Cap1 or Cap2 form, depending on the presence of 2'-O-methylation on the first transcribed nucleotide or both the first and second transcribed nucleotides, respectively1,2. However, the identity of Cap2-containing mRNAs and the function of Cap2 are unclear. Here we describe CLAM-Cap-seq, a method for transcriptome-wide mapping and quantification of Cap2. We find that unlike other epitranscriptomic modifications, Cap2 can occur on all mRNAs. Cap2 is formed through a slow continuous conversion of mRNAs from Cap1 to Cap2 as mRNAs age in the cytosol. As a result, Cap2 is enriched on long-lived mRNAs. Large increases in the abundance of Cap1 leads to activation of RIG-I, especially in conditions in which expression of RIG-I is increased. The methylation of Cap1 to Cap2 markedly reduces the ability of RNAs to bind to and activate RIG-I. The slow methylation rate of Cap2 allows Cap2 to accumulate on host mRNAs, yet ensures that low levels of Cap2 occur on newly expressed viral RNAs. Overall, these results reveal an immunostimulatory role for Cap1, and that Cap2 functions to reduce activation of the innate immune response.
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Affiliation(s)
- Vladimir Despic
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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23
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TMPRSS2 Is Essential for SARS-CoV-2 Beta and Omicron Infection. Viruses 2023; 15:v15020271. [PMID: 36851486 PMCID: PMC9961888 DOI: 10.3390/v15020271] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
The COVID-19 pandemic remains a global health threat and novel antiviral strategies are urgently needed. SARS-CoV-2 employs the cellular serine protease TMPRSS2 for entry into lung cells, and TMPRSS2 inhibitors are being developed for COVID-19 therapy. However, the SARS-CoV-2 Omicron variant, which currently dominates the pandemic, prefers the endo/lysosomal cysteine protease cathepsin L over TMPRSS2 for cell entry, raising doubts as to whether TMPRSS2 inhibitors would be suitable for the treatment of patients infected with the Omicron variant. Nevertheless, the contribution of TMPRSS2 to the spread of SARS-CoV-2 in the infected host is largely unclear. In this study, we show that the loss of TMPRSS2 strongly reduced the replication of the Beta variant in the nose, trachea and lung of C57BL/6 mice, and protected the animals from weight loss and disease. The infection of mice with the Omicron variant did not cause disease, as expected, but again, TMPRSS2 was essential for efficient viral spread in the upper and lower respiratory tract. These results identify the key role of TMPRSS2 in SARS-CoV-2 Beta and Omicron infection, and highlight TMPRSS2 as an attractive target for antiviral intervention.
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McKellar J, Arnaud-Arnould M, Chaloin L, Tauziet M, Arpin-André C, Pourcelot O, Blaise M, Moncorgé O, Goujon C. An evolutionarily conserved N-terminal leucine is essential for MX1 GTPase antiviral activity against different families of RNA viruses. J Biol Chem 2023; 299:102747. [PMID: 36436557 PMCID: PMC9808005 DOI: 10.1016/j.jbc.2022.102747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/27/2022] Open
Abstract
Myxovirus resistance protein 1 (MX1) and MX2 are homologous, dynamin-like large GTPases, induced upon interferon exposure. Human MX1 (HsMX1) is known to inhibit many viruses, including influenza A virus, by likely acting at various steps of their life cycles. Despite decades of studies, the mechanism(s) of action with which MX1 proteins manage to inhibit target viruses is not fully understood. MX1 proteins are mechano-enzymes and share a similar organization to dynamin, with a GTPase domain and a carboxy-terminal stalk domain, connected by a bundle signaling element. These three elements are known to be essential for antiviral activity. HsMX1 has two unstructured regions, the L4 loop, also essential for antiviral activity, and a short amino (N)-terminal region, which greatly varies between MX1 proteins of different species. The role of this N-terminal domain in antiviral activity is not known. Herein, using mutagenesis, imaging, and biochemical approaches, we demonstrate that the N-terminal domain of HsMX1 is essential for antiviral activity against influenza A virus, Vesicular Stomatitis Virus, and La Crosse virus. Furthermore, we pinpoint a highly conserved leucine within this region, which is absolutely crucial for human, mouse, and bat MX1 protein antiviral activity. Importantly, mutation of this leucine does not compromise GTPase activity or oligomerization capabilities but does modify MX1 protein subcellular localization. The discovery of this essential and highly conserved residue defines this region as key for antiviral activity and may reveal insights as to the mechanism(s) of action of MX1 proteins.
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Affiliation(s)
- Joe McKellar
- IRIM, CNRS, Montpellier University, Montpellier, France
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25
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Inhibition of p38 signaling curtails the SARS-CoV-2 induced inflammatory response but retains the IFN-dependent antiviral defense of the lung epithelial barrier. Antiviral Res 2023; 209:105475. [PMID: 36423831 PMCID: PMC9677559 DOI: 10.1016/j.antiviral.2022.105475] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/18/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022]
Abstract
SARS-CoV-2 is the causative agent of the immune response-driven disease COVID-19 for which new antiviral and anti-inflammatory treatments are urgently needed to reduce recovery time, risk of death and long COVID development. Here, we demonstrate that the immunoregulatory kinase p38 MAPK is activated during viral entry, mediated by the viral spike protein, and drives the harmful virus-induced inflammatory responses. Using primary human lung explants and lung epithelial organoids, we demonstrate that targeting p38 signal transduction with the selective and clinically pre-evaluated inhibitors PH-797804 and VX-702 markedly reduced the expression of the pro-inflammatory cytokines IL6, CXCL8, CXCL10 and TNF-α during infection, while viral replication and the interferon-mediated antiviral response of the lung epithelial barrier were largely maintained. Furthermore, our results reveal a high level of drug synergism of both p38 inhibitors in co-treatments with the nucleoside analogs Remdesivir and Molnupiravir to suppress viral replication of the SARS-CoV-2 variants of concern, revealing an exciting and novel mode of synergistic action of p38 inhibition. These results open new avenues for the improvement of the current treatment strategies for COVID-19.
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26
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Muik A, Lui BG, Bacher M, Wallisch AK, Toker A, Couto CIC, Güler A, Mampilli V, Schmitt GJ, Mottl J, Ziegenhals T, Fesser S, Reinholz J, Wernig F, Schraut KG, Hefesha H, Cai H, Yang Q, Walzer KC, Grosser J, Strauss S, Finlayson A, Krüger K, Ozhelvaci O, Grikscheit K, Kohmer N, Ciesek S, Swanson KA, Vogel AB, Türeci Ö, Sahin U. Exposure to BA.4/5 S protein drives neutralization of Omicron BA.1, BA.2, BA.2.12.1, and BA.4/5 in vaccine-experienced humans and mice. Sci Immunol 2022; 7:eade9888. [PMID: 36378074 PMCID: PMC9765452 DOI: 10.1126/sciimmunol.ade9888] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The SARS-CoV-2 Omicron variant and its sublineages show pronounced viral escape from neutralizing antibodies elicited by vaccination or prior SARS-CoV-2 variant infection owing to over 30-amino acid alterations within the spike (S) glycoprotein. Breakthrough infection of vaccinated individuals with Omicron sublineages BA.1 and BA.2 is associated with distinct patterns of cross-neutralizing activity against SARS-CoV-2 variants of concern (VOCs). In continuation of our previous work, we characterized the effect of Omicron BA.4/BA.5 S glycoprotein exposure on the neutralizing antibody response upon breakthrough infection in vaccinated individuals and upon variant-adapted booster vaccination in mice. We found that immune sera from triple mRNA-vaccinated individuals with subsequent breakthrough infection during the Omicron BA.4/BA.5 wave showed cross-neutralizing activity against previous Omicron variants BA.1, BA.2, BA.2.12.1, and BA.4/BA.5 itself. Administration of a prototypic BA.4/BA.5-adapted mRNA booster vaccine to mice after SARS-CoV-2 wild-type strain-based primary immunization is associated with broader cross-neutralizing activity than a BA.1-adapted booster. Whereas the Omicron BA.1-adapted mRNA vaccine in a bivalent format (wild-type + BA.1) broadens cross-neutralizing activity relative to the BA.1 monovalent booster, cross-neutralization of BA.2 and descendants is more effective in mice boosted with a bivalent wild-type + BA.4/BA.5 vaccine. In naïve mice, primary immunization with the bivalent wild-type + Omicron BA.4/BA.5 vaccine induces strong cross-neutralizing activity against Omicron VOCs and previous variants. These findings suggest that, when administered as boosters, mono- and bivalent Omicron BA.4/BA.5-adapted vaccines enhance neutralization breadth and that the bivalent version also has the potential to confer protection to individuals with no preexisting immunity against SARS-CoV-2.
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Affiliation(s)
| | | | - Maren Bacher
- BioNTech, An der Goldgrube 12, 55131 Mainz, Germany
| | | | - Aras Toker
- BioNTech, An der Goldgrube 12, 55131 Mainz, Germany
| | | | | | | | | | | | | | | | | | | | | | | | - Hui Cai
- Pfizer, 401 N. Middletown Rd., Pearl River, NY 10960, USA
| | - Qi Yang
- Pfizer, 401 N. Middletown Rd., Pearl River, NY 10960, USA
| | | | | | | | | | | | | | - Katharina Grikscheit
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Niko Kohmer
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany.,DZIF – German Centre for Infection Research, External Partner Site, 60596 Frankfurt am Main, Germany
| | | | | | - Özlem Türeci
- BioNTech, An der Goldgrube 12, 55131 Mainz, Germany.,HI-TRON – Helmholtz Institute for Translational Oncology Mainz by DKFZ, Obere Zahlbacherstr. 63, 55131 Mainz, Germany
| | - Ugur Sahin
- BioNTech, An der Goldgrube 12, 55131 Mainz, Germany.,TRON gGmbH – Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Freiligrathstraße 12, 55131 Mainz, Germany.,Corresponding author.
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27
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Taddeo A, Veiga IB, Devisme C, Boss R, Plattet P, Weigang S, Kochs G, Thiel V, Benarafa C, Zimmer G. Optimized intramuscular immunization with VSV-vectored spike protein triggers a superior immune response to SARS-CoV-2. NPJ Vaccines 2022; 7:82. [PMID: 35879345 PMCID: PMC9309237 DOI: 10.1038/s41541-022-00508-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 06/21/2022] [Indexed: 11/09/2022] Open
Abstract
Immunization with vesicular stomatitis virus (VSV)-vectored COVID-19 vaccine candidates expressing the SARS-CoV-2 spike protein in place of the VSV glycoprotein relies implicitly on expression of the ACE2 receptor at the muscular injection site. Here, we report that such a viral vector vaccine did not induce protective immunity following intramuscular immunization of K18-hACE2 transgenic mice. However, when the viral vector was trans-complemented with the VSV glycoprotein, intramuscular immunization resulted in high titers of spike-specific neutralizing antibodies. The vaccinated animals were fully protected following infection with a lethal dose of SARS-CoV-2-SD614G via the nasal route, and partially protected if challenged with the SARS-CoV-2Delta variant. While dissemination of the challenge virus to the brain was completely inhibited, replication in the lung with consequent lung pathology was not entirely controlled. Thus, intramuscular immunization was clearly enhanced by trans-complementation of the VSV-vectored vaccines by the VSV glycoprotein and led to protection from COVID-19, although not achieving sterilizing immunity.
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28
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Dang W, Li T, Xu F, Wang Y, Yang F, Zheng H. Establishment of a CRISPR/Cas9 knockout library for screening type I interferon-inducible antiviral effectors in pig cells. Front Immunol 2022; 13:1016545. [PMID: 36505425 PMCID: PMC9732717 DOI: 10.3389/fimmu.2022.1016545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/26/2022] [Indexed: 11/26/2022] Open
Abstract
Diseases caused by emerging swine viruses had a great economic impact, constituting a new challenge for researchers and practicing veterinarians. Innate immune control of viral pathogen invasion is mediated by interferons (IFNs), resulting in transcriptional elevation of hundreds of IFN-stimulated genes (ISGs). However, the ISG family is vast and species-specific, and despite remarkable advancements in uncovering the breadth of IFN-induced gene expression in mouse and human, it is less characterized with respect to the repertoire of porcine ISGs and their functional annotation. Herein, with the application of RNA-sequencing (RNA-Seq) gene profiling, the breadth of IFN-induced gene expression in the context of type I IFN stimulation was explored by using IBRS-2 cell, a commonly used high-efficient cultivation system for porcine picornaviruses. By establishing inclusion criteria, a total of 359 ISGs were selected. Aiming to identify key effectors mediating type I IFN inhibition of swine viruses, a CRISPR/Cas9 knockout library of 1908 sgRNAs targeting 5' constitutive exons of 359 ISGs with an average of 5 to 6 sgRNAs per gene was constructed. Using VSV-eGFP (vesicular stomatitis virus, fused with GFP) as a model virus, a subset of highest-ranking candidates were identified, including previously validated anti-VSV genes IRF9, IFITM3, LOC100519082 and REC8, as well as several novel hits. This approach attains a high level of feasibility and reliability, and a high rate of hit identification, providing a forward-looking platform to systematically profile the effectors of type I IFN antiviral response against porcine viruses.
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Affiliation(s)
- Wen Dang
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Tao Li
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Fan Xu
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yannan Wang
- Lanzhou University Second Hospital, Department of Radiology, Lanzhou, China
| | - Fan Yang
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China,*Correspondence: Haixue Zheng,
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29
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Jacobsen H, Strengert M, Maaß H, Ynga Durand MA, Katzmarzyk M, Kessel B, Harries M, Rand U, Abassi L, Kim Y, Lüddecke T, Metzdorf K, Hernandez P, Ortmann J, Heise JK, Castell S, Gornyk D, Glöckner S, Melhorn V, Kemmling Y, Lange B, Dulovic A, Marsall P, Häring J, Junker D, Schneiderhan-Marra N, Hoffmann M, Pöhlmann S, Krause G, Cicin-Sain L. Diminished neutralization responses towards SARS-CoV-2 Omicron VoC after mRNA or vector-based COVID-19 vaccinations. Sci Rep 2022; 12:19858. [PMID: 36400804 PMCID: PMC9673895 DOI: 10.1038/s41598-022-22552-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 10/17/2022] [Indexed: 11/19/2022] Open
Abstract
SARS-CoV-2 variants accumulating immune escape mutations provide a significant risk to vaccine-induced protection against infection. The novel variant of concern (VoC) Omicron BA.1 and its sub-lineages have the largest number of amino acid alterations in its Spike protein to date. Thus, they may efficiently escape recognition by neutralizing antibodies, allowing breakthrough infections in convalescent and vaccinated individuals in particular in those who have only received a primary immunization scheme. We analyzed neutralization activity of sera from individuals after vaccination with all mRNA-, vector- or heterologous immunization schemes currently available in Europe by in vitro neutralization assay at peak response towards SARS-CoV-2 B.1, Omicron sub-lineages BA.1, BA.2, BA.2.12.1, BA.3, BA.4/5, Beta and Delta pseudotypes and also provide longitudinal follow-up data from BNT162b2 vaccinees. All vaccines apart from Ad26.CoV2.S showed high levels of responder rates (96-100%) towards the SARS-CoV-2 B.1 isolate, and minor to moderate reductions in neutralizing Beta and Delta VoC pseudotypes. The novel Omicron variant and its sub-lineages had the biggest impact, both in terms of response rates and neutralization titers. Only mRNA-1273 showed a 100% response rate to Omicron BA.1 and induced the highest level of neutralizing antibody titers, followed by heterologous prime-boost approaches. Homologous BNT162b2 vaccination, vector-based AZD1222 and Ad26.CoV2.S performed less well with peak responder rates of 48%, 56% and 9%, respectively. However, Omicron responder rates in BNT162b2 recipients were maintained in our six month longitudinal follow-up indicating that individuals with cross-protection against Omicron maintain it over time. Overall, our data strongly argue for booster doses in individuals who were previously vaccinated with BNT162b2, or a vector-based primary immunization scheme.
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Affiliation(s)
- Henning Jacobsen
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Monika Strengert
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- TWINCORE, Centre for Experimental and Clinical Infection Research, Joint Venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Henrike Maaß
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Maeva Katzmarzyk
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Barbora Kessel
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Manuela Harries
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ulfert Rand
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Leila Abassi
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Yeonsu Kim
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Tatjana Lüddecke
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Kristin Metzdorf
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Pilar Hernandez
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Julia Ortmann
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jana-Kristin Heise
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stefanie Castell
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Daniela Gornyk
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stephan Glöckner
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Vanessa Melhorn
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Yvonne Kemmling
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Berit Lange
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Alex Dulovic
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Patrick Marsall
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Julia Häring
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Daniel Junker
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | | | - Markus Hoffmann
- Deutsches Primatenzentrum, Leibniz-Institut Für Primatenforschung, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University, Göttingen, Germany
| | - Stefan Pöhlmann
- Deutsches Primatenzentrum, Leibniz-Institut Für Primatenforschung, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University, Göttingen, Germany
| | - Gérard Krause
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
- TWINCORE, Centre for Experimental and Clinical Infection Research, Joint Venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany.
| | - Luka Cicin-Sain
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany.
- Centre for Individualized Infection Medicine (CIIM), Joint Venture of Helmholtz Centre for Infection Research and Medical School Hannover, Inhoffenstraße 7, 38124, Braunschweig, Germany.
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The SARS-CoV-2 Delta-Omicron Recombinant Lineage (XD) Exhibits Immune-Escape Properties Similar to the Omicron (BA.1) Variant. Int J Mol Sci 2022; 23:ijms232214057. [PMID: 36430535 PMCID: PMC9696394 DOI: 10.3390/ijms232214057] [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: 10/24/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Recently, a recombinant SARS-CoV-2 lineage, XD, emerged that harbors a spike gene that is largely derived from the Omicron variant BA.1 in the genetic background of the Delta variant. This finding raised concerns that the recombinant virus might exhibit altered biological properties as compared to the parental viruses and might pose an elevated threat to human health. Here, using pseudotyped particles, we show that ACE2 binding and cell tropism of XD mimics that of BA.1. Further, XD and BA.1 displayed comparable sensitivity to neutralization by antibodies induced upon vaccination with BNT162b2/Comirnaty (BNT) or BNT vaccination followed by breakthrough infection. Our findings reveal important biological commonalities between XD and Omicron BA.1 host cell entry and its inhibition by antibodies.
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31
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Host Cell Entry and Neutralization Sensitivity of SARS-CoV-2 Lineages B.1.620 and R.1. Viruses 2022; 14:v14112475. [PMID: 36366573 PMCID: PMC9698971 DOI: 10.3390/v14112475] [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: 10/13/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) facilitates viral entry into host cells and is the key target for neutralizing antibodies. The SARS-CoV-2 lineage B.1.620 carries fifteen mutations in the S protein and is spread in Africa, the US and Europe, while lineage R.1 harbors four mutations in S and infections were observed in several countries, particularly Japan and the US. However, the impact of the mutations in B.1.620 and R.1 S proteins on antibody-mediated neutralization and host cell entry are largely unknown. Here, we report that these mutations are compatible with robust ACE2 binding and entry into cell lines, and they markedly reduce neutralization by vaccine-induced antibodies. Our results reveal evasion of neutralizing antibodies by B.1.620 and R.1, which might have contributed to the spread of these lineages.
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32
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Balkrishna A, Goswami S, Singh H, Gohel V, Dev R, Haldar S, Varshney A. Herbo-mineral formulation, Divya-Swasari-Vati averts SARS-CoV-2 pseudovirus entry into human alveolar epithelial cells by interfering with spike protein-ACE 2 interaction and IL-6/TNF-α /NF-κB signaling. Front Pharmacol 2022; 13:1024830. [PMID: 36386162 PMCID: PMC9643876 DOI: 10.3389/fphar.2022.1024830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/06/2022] [Indexed: 08/16/2023] Open
Abstract
The herbo-mineral formulation, Divya-Swasari-Vati (DSV), is a well-known Ayurvedic medication for respiratory ailments. In a recent pre-clinical study, DSV rescued humanized zebrafish from SARS-CoV-2 S-protein-induced pathologies. This merited for an independent evaluation of DSV as a SARS-CoV-2 entry inhibitor in the human host cell and its effectiveness in ameliorating associated cytokine production. The ELISA-based protein-protein interaction study showed that DSV inhibited the interactions of recombinant human ACE 2 with three different variants of S proteins, namely, Smut 1 (the first reported variant), Smut 2 (W436R variant) and Smut 3 (D614G variant). Entry of recombinant vesicular stomatitis SARS-CoV-2 (VSVppSARS-2S) pseudovirus, having firefly luciferase and EGFP reporters, was assessed through luciferase assay and fluorescent microscopy. DSV exhibited dose-dependent inhibition of VSVppSARS-2S pseudovirus entry into human lung epithelial A549 cells and also suppressed elevated levels of secreted pro-inflammatory cytokines such as interleukin-6 (IL-6), interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α) induced by viral infection mimicking Poly I:C-, S-protein- and VSVppSARS-2S pseudovirus. In human immune cells, DSV also moderated TNF-α-mediated NF-κB induction, in a dose-dependent manner. The observed anti-viral effect of DSV against SARS-CoV-2 is attributable to the presence of different metabolites Summarily, the observations from this study biochemically demonstrated that DSV interfered with the interaction between SARS-CoV-2 S-protein and human ACE 2 receptor which consequently, inhibited viral entry into the host cells and concomitant induction of inflammatory response.
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Affiliation(s)
- Acharya Balkrishna
- Drug Discovery and Development Division, Patanjali Research Institute, Haridwar, Uttarakhand, India
- Department of Allied and Applied Sciences, University of Patanjali, Haridwar, Uttarakhand, India
| | - Sudeep Goswami
- Drug Discovery and Development Division, Patanjali Research Institute, Haridwar, Uttarakhand, India
| | - Hoshiyar Singh
- Drug Discovery and Development Division, Patanjali Research Institute, Haridwar, Uttarakhand, India
| | - Vivek Gohel
- Drug Discovery and Development Division, Patanjali Research Institute, Haridwar, Uttarakhand, India
| | - Rishabh Dev
- Drug Discovery and Development Division, Patanjali Research Institute, Haridwar, Uttarakhand, India
| | - Swati Haldar
- Drug Discovery and Development Division, Patanjali Research Institute, Haridwar, Uttarakhand, India
| | - Anurag Varshney
- Drug Discovery and Development Division, Patanjali Research Institute, Haridwar, Uttarakhand, India
- Department of Allied and Applied Sciences, University of Patanjali, Haridwar, Uttarakhand, India
- Special Centre for Systems Medicine, Jawaharlal Nehru University, New Delhi, India
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33
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Bonaventure B, Rebendenne A, Chaves Valadão AL, Arnaud‐Arnould M, Gracias S, Garcia de Gracia F, McKellar J, Labaronne E, Tauziet M, Vivet‐Boudou V, Bernard E, Briant L, Gros N, Djilli W, Courgnaud V, Parrinello H, Rialle S, Blaise M, Lacroix L, Lavigne M, Paillart J, Ricci EP, Schulz R, Jouvenet N, Moncorgé O, Goujon C. The
DEAD
box
RNA
helicase
DDX42
is an intrinsic inhibitor of positive‐strand
RNA
viruses. EMBO Rep 2022; 23:e54061. [PMID: 36161446 PMCID: PMC9638865 DOI: 10.15252/embr.202154061] [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: 09/28/2021] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 11/29/2022] Open
Abstract
Genome‐wide screens are powerful approaches to unravel regulators of viral infections. Here, a CRISPR screen identifies the RNA helicase DDX42 as an intrinsic antiviral inhibitor of HIV‐1. Depletion of endogenous DDX42 increases HIV‐1 DNA accumulation and infection in cell lines and primary cells. DDX42 overexpression inhibits HIV‐1 infection, whereas expression of a dominant‐negative mutant increases infection. Importantly, DDX42 also restricts LINE‐1 retrotransposition and infection with other retroviruses and positive‐strand RNA viruses, including CHIKV and SARS‐CoV‐2. However, DDX42 does not impact the replication of several negative‐strand RNA viruses, arguing against an unspecific effect on target cells, which is confirmed by RNA‐seq analysis. Proximity ligation assays show DDX42 in the vicinity of viral elements, and cross‐linking RNA immunoprecipitation confirms a specific interaction of DDX42 with RNAs from sensitive viruses. Moreover, recombinant DDX42 inhibits HIV‐1 reverse transcription in vitro. Together, our data strongly suggest a direct mode of action of DDX42 on viral ribonucleoprotein complexes. Our results identify DDX42 as an intrinsic viral inhibitor, opening new perspectives to target the life cycle of numerous RNA viruses.
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Affiliation(s)
| | | | | | | | - Ségolène Gracias
- Virus Sensing and Signaling Unit, Department of Virology, Institut Pasteur Université de Paris Cité, CNRS UMR 3569 Paris France
| | | | | | | | | | - Valérie Vivet‐Boudou
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002 Strasbourg France
| | | | | | - Nathalie Gros
- CEMIPAI, CNRS Université de Montpellier Montpellier France
| | | | | | - Hugues Parrinello
- Montpellier GenomiX (MGX), Biocampus, CNRS, INSERM Université de Montpellier Montpellier France
| | - Stéphanie Rialle
- Montpellier GenomiX (MGX), Biocampus, CNRS, INSERM Université de Montpellier Montpellier France
| | | | - Laurent Lacroix
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM Université PSL Paris France
| | - Marc Lavigne
- Department of Virology Institut Pasteur Paris France
| | | | | | - Reiner Schulz
- Department of Medical & Molecular Genetics King's College London London UK
| | - Nolwenn Jouvenet
- Virus Sensing and Signaling Unit, Department of Virology, Institut Pasteur Université de Paris Cité, CNRS UMR 3569 Paris France
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34
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Wettstein L, Immenschuh P, Weil T, Conzelmann C, Almeida‐Hernández Y, Hoffmann M, Kempf A, Nehlmeier I, Lotke R, Petersen M, Stenger S, Kirchhoff F, Sauter D, Pöhlmann S, Sanchez‐Garcia E, Münch J. Native and activated antithrombin inhibits TMPRSS2 activity and SARS-CoV-2 infection. J Med Virol 2022; 95:e28124. [PMID: 36056630 PMCID: PMC9538173 DOI: 10.1002/jmv.28124] [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] [Received: 07/20/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 01/11/2023]
Abstract
Host cell proteases such as TMPRSS2 are critical determinants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) tropism and pathogenesis. Here, we show that antithrombin (AT), an endogenous serine protease inhibitor regulating coagulation, is a broad-spectrum inhibitor of coronavirus infection. Molecular docking and enzyme activity assays demonstrate that AT binds and inhibits TMPRSS2, a serine protease that primes the Spike proteins of coronaviruses for subsequent fusion. Consequently, AT blocks entry driven by the Spikes of SARS-CoV, MERS-CoV, hCoV-229E, SARS-CoV-2 and its variants of concern including Omicron, and suppresses lung cell infection with genuine SARS-CoV-2. Thus, AT is an endogenous inhibitor of SARS-CoV-2 that may be involved in COVID-19 pathogenesis. We further demonstrate that activation of AT by anticoagulants, such as heparin or fondaparinux, increases the anti-TMPRSS2 and anti-SARS-CoV-2 activity of AT, suggesting that repurposing of native and activated AT for COVID-19 treatment should be explored.
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Affiliation(s)
- Lukas Wettstein
- Institute of Molecular VirologyUlm University Medical CenterUlmGermany
| | | | - Tatjana Weil
- Institute of Molecular VirologyUlm University Medical CenterUlmGermany
| | - Carina Conzelmann
- Institute of Molecular VirologyUlm University Medical CenterUlmGermany
| | - Yasser Almeida‐Hernández
- Computational Biochemistry, Center of Medical BiotechnologyUniversity of Duisburg‐EssenEssenGermany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center‐Leibniz Institute for Primate ResearchGöttingenGermany,Faculty of Biology and PsychologyGeorg‐August‐UniversityGöttingenGermany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center‐Leibniz Institute for Primate ResearchGöttingenGermany,Faculty of Biology and PsychologyGeorg‐August‐UniversityGöttingenGermany
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center‐Leibniz Institute for Primate ResearchGöttingenGermany
| | - Rishikesh Lotke
- Institute for Medical Virology and Epidemiology of Viral DiseasesUniversity Hospital TübingenTübingenGermany
| | - Moritz Petersen
- Institute for Medical Virology and Epidemiology of Viral DiseasesUniversity Hospital TübingenTübingenGermany
| | - Steffen Stenger
- Institute for Microbiology and HygieneUlm University Medical CenterUlmGermany
| | - Frank Kirchhoff
- Institute of Molecular VirologyUlm University Medical CenterUlmGermany
| | - Daniel Sauter
- Institute for Medical Virology and Epidemiology of Viral DiseasesUniversity Hospital TübingenTübingenGermany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center‐Leibniz Institute for Primate ResearchGöttingenGermany,Faculty of Biology and PsychologyGeorg‐August‐UniversityGöttingenGermany
| | - Elsa Sanchez‐Garcia
- Computational Biochemistry, Center of Medical BiotechnologyUniversity of Duisburg‐EssenEssenGermany
| | - Jan Münch
- Institute of Molecular VirologyUlm University Medical CenterUlmGermany
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35
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The Bovine Seminal Plasma Protein PDC-109 Possesses Pan-Antiviral Activity. Viruses 2022; 14:v14092031. [PMID: 36146836 PMCID: PMC9504757 DOI: 10.3390/v14092031] [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: 08/22/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
Mammalian seminal plasma contains a multitude of bioactive components, including lipids, glucose, mineral elements, metabolites, proteins, cytokines, and growth factors, with various functions during insemination and fertilization. The seminal plasma protein PDC-109 is one of the major soluble components of the bovine ejaculate and is crucially important for sperm motility, capacitation, and acrosome reaction. A hitherto underappreciated function of seminal plasma is its anti-microbial and antiviral activity, which may limit the sexual transmission of infectious diseases during intercourse. We have recently discovered that PDC-109 inhibits the membrane fusion activity of influenza virus particles and significantly impairs viral infections at micromolar concentrations. Here we investigated whether the antiviral activity of PDC-109 is restricted to Influenza or if other mammalian viruses are similarly affected. We focused on Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), the etiological agent of the Coronavirus Disease 19 (COVID-19), thoroughly assessing PDC-109 inhibition with SARS-CoV-2 Spike (S)-pseudotyped reporter virus particles, but also live-virus infections. Consistent with our previous publications, we found significant virus inhibition, albeit accompanied by substantial cytotoxicity. However, using time-of-addition experiments we discovered a treatment regimen that enables virus suppression without affecting cell viability. We furthermore demonstrated that PDC-109 is also able to impair infections mediated by the VSV glycoprotein (VSVg), thus indicating a broad pan-antiviral activity against multiple virus species and families.
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36
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Seidel A, Zanoni M, Groß R, Krnavek D, Erdemci-Evin S, von Maltitz P, Albers DPJ, Conzelmann C, Liu S, Weil T, Mayer B, Hoffmann M, Pöhlmann S, Beil A, Kroschel J, Kirchhoff F, Münch J, Müller JA. BNT162b2 booster after heterologous prime-boost vaccination induces potent neutralizing antibodies and T cell reactivity against SARS-CoV-2 Omicron BA.1 in young adults. Front Immunol 2022; 13:882918. [PMID: 35958601 PMCID: PMC9357986 DOI: 10.3389/fimmu.2022.882918] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/28/2022] [Indexed: 01/14/2023] Open
Abstract
In light of the decreasing immune protection against symptomatic SARS-CoV-2 infection after initial vaccinations and the now dominant immune-evasive Omicron variants, 'booster' vaccinations are regularly performed to restore immune responses. Many individuals have received a primary heterologous prime-boost vaccination with long intervals between vaccinations, but the resulting long-term immunity and the effects of a subsequent 'booster', particularly against Omicron BA.1, have not been defined. We followed a cohort of 23 young adults, who received a primary heterologous ChAdOx1 nCoV-19 BNT162b2 prime-boost vaccination, over a 7-month period and analysed how they responded to a BNT162b2 'booster'. We show that already after the primary heterologous vaccination, neutralization titers against Omicron BA.1 are recognizable but that humoral and cellular immunity wanes over the course of half a year. Residual responsive memory T cells recognized spike epitopes of the early SARS-CoV-2 B.1 strain as well as the Delta and BA.1 variants of concern (VOCs). However, the remaining antibody titers hardly neutralized these VOCs. The 'booster' vaccination was well tolerated and elicited both high antibody titers and increased memory T cell responses against SARS-CoV-2 including BA.1. Strikingly, in this young heterologously vaccinated cohort the neutralizing activity after the 'booster' was almost as potent against BA.1 as against the early B.1 strain. Our results suggest that a 'booster' after heterologous vaccination results in effective immune maturation and potent protection against the Omicron BA.1 variant in young adults.
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Affiliation(s)
- Alina Seidel
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Michelle Zanoni
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Rüdiger Groß
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Daniela Krnavek
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | | | - Pascal von Maltitz
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Dan P. J. Albers
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Carina Conzelmann
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Sichen Liu
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Tatjana Weil
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Benjamin Mayer
- Institute for Epidemiology and Medical Biometry, Ulm University, Ulm, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center – Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center – Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Alexandra Beil
- Central Department for Clinical Chemistry, University Hospital Ulm, Ulm, Germany
| | - Joris Kroschel
- Central Department for Clinical Chemistry, University Hospital Ulm, Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
- Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm, Germany
| | - Janis A. Müller
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
- Institute of Virology, Philipps University of Marburg, Marburg, Germany
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37
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Rebendenne A, Roy P, Bonaventure B, Chaves Valadão AL, Desmarets L, Arnaud-Arnould M, Rouillé Y, Tauziet M, Giovannini D, Touhami J, Lee Y, DeWeirdt P, Hegde M, Urbach S, Koulali KE, de Gracia FG, McKellar J, Dubuisson J, Wencker M, Belouzard S, Moncorgé O, Doench JG, Goujon C. Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal HCoVs. Nat Genet 2022; 54:1090-1102. [PMID: 35879413 DOI: 10.1038/s41588-022-01110-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 05/26/2022] [Indexed: 12/23/2022]
Abstract
CRISPR knockout (KO) screens have identified host factors regulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication. Here, we conducted a meta-analysis of these screens, which showed a high level of cell-type specificity of the identified hits, highlighting the necessity of additional models to uncover the full landscape of host factors. Thus, we performed genome-wide KO and activation screens in Calu-3 lung cells and KO screens in Caco-2 colorectal cells, followed by secondary screens in four human cell lines. This revealed host-dependency factors, including AP1G1 adaptin and ATP8B1 flippase, as well as inhibitors, including mucins. Interestingly, some of the identified genes also modulate Middle East respiratory syndrome coronavirus (MERS-CoV) and seasonal human coronavirus (HCoV) (HCoV-NL63 and HCoV-229E) replication. Moreover, most genes had an impact on viral entry, with AP1G1 likely regulating TMPRSS2 activity at the plasma membrane. These results demonstrate the value of multiple cell models and perturbational modalities for understanding SARS-CoV-2 replication and provide a list of potential targets for therapeutic interventions.
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Affiliation(s)
| | - Priyanka Roy
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Lowiese Desmarets
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Lille, France
| | | | - Yves Rouillé
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Lille, France
| | | | - Donatella Giovannini
- IGMM, CNRS, Montpellier University, Montpellier, France.,Metafora Biosystems, Paris, France
| | - Jawida Touhami
- IGMM, CNRS, Montpellier University, Montpellier, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Yenarae Lee
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mudra Hegde
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Serge Urbach
- IGF, Montpellier University, CNRS, INSERM, Montpellier, France
| | | | | | - Joe McKellar
- IRIM, CNRS, Montpellier University, Montpellier, France
| | - Jean Dubuisson
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Lille, France
| | | | - Sandrine Belouzard
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Lille, France
| | | | - John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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38
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Callegari I, Schneider M, Berloffa G, Mühlethaler T, Holdermann S, Galli E, Roloff T, Boss R, Infanti L, Khanna N, Egli A, Buser A, Zimmer G, Derfuss T, Sanderson NSR. Potent neutralization by monoclonal human IgM against SARS-CoV-2 is impaired by class switch. EMBO Rep 2022; 23:e53956. [PMID: 35548920 PMCID: PMC9253785 DOI: 10.15252/embr.202153956] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 04/13/2022] [Accepted: 04/27/2022] [Indexed: 01/11/2023] Open
Abstract
To investigate the class‐dependent properties of anti‐viral IgM antibodies, we use membrane antigen capture activated cell sorting to isolate spike‐protein‐specific B cells from donors recently infected with SARS‐CoV‐2, allowing production of recombinant antibodies. We isolate 20, spike‐protein‐specific antibodies of classes IgM, IgG, and IgA, none of which shows any antigen‐independent binding to human cells. Two antibodies of class IgM mediate virus neutralization at picomolar concentrations, but this potency is lost following artificial switch to IgG. Although, as expected, the IgG versions of the antibodies appear to have lower avidity than their IgM parents, this is not sufficient to explain the loss of potency.
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Affiliation(s)
- Ilaria Callegari
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland.,MS Center, Neurologic Clinic and Policlinic, Research Center for Clinical Neuroimmunology and Neuroscience Basel (RC2NB), University Hospital Basel, University of Basel, Basel, Switzerland
| | - Mika Schneider
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Giuliano Berloffa
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Tobias Mühlethaler
- Biophysics Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Sebastian Holdermann
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland.,MS Center, Neurologic Clinic and Policlinic, Research Center for Clinical Neuroimmunology and Neuroscience Basel (RC2NB), University Hospital Basel, University of Basel, Basel, Switzerland
| | - Edoardo Galli
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland.,MS Center, Neurologic Clinic and Policlinic, Research Center for Clinical Neuroimmunology and Neuroscience Basel (RC2NB), University Hospital Basel, University of Basel, Basel, Switzerland
| | - Tim Roloff
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Renate Boss
- Federal Food Safety and Veterinary Office, Bern, Switzerland
| | - Laura Infanti
- Regional Blood Transfusion Service, Swiss Red Cross, Basel, Switzerland
| | - Nina Khanna
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Andreas Buser
- Regional Blood Transfusion Service, Swiss Red Cross, Basel, Switzerland
| | - Gert Zimmer
- Institute of Virology and Immunology, Bern & Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Tobias Derfuss
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland.,MS Center, Neurologic Clinic and Policlinic, Research Center for Clinical Neuroimmunology and Neuroscience Basel (RC2NB), University Hospital Basel, University of Basel, Basel, Switzerland
| | - Nicholas S R Sanderson
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland.,MS Center, Neurologic Clinic and Policlinic, Research Center for Clinical Neuroimmunology and Neuroscience Basel (RC2NB), University Hospital Basel, University of Basel, Basel, Switzerland
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39
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Groß R, Dias Loiola LM, Issmail L, Uhlig N, Eberlein V, Conzelmann C, Olari L, Rauch L, Lawrenz J, Weil T, Müller JA, Cardoso MB, Gilg A, Larsson O, Höglund U, Pålsson SA, Tvilum AS, Løvschall KB, Kristensen MM, Spetz A, Hontonnou F, Galloux M, Grunwald T, Zelikin AN, Münch J. Macromolecular Viral Entry Inhibitors as Broad-Spectrum First-Line Antivirals with Activity against SARS-CoV-2. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201378. [PMID: 35543527 PMCID: PMC9284172 DOI: 10.1002/advs.202201378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/11/2022] [Indexed: 05/03/2023]
Abstract
Inhibitors of viral cell entry based on poly(styrene sulfonate) and its core-shell nanoformulations based on gold nanoparticles are investigated against a panel of viruses, including clinical isolates of SARS-CoV-2. Macromolecular inhibitors are shown to exhibit the highly sought-after broad-spectrum antiviral activity, which covers most analyzed enveloped viruses and all of the variants of concern for SARS-CoV-2 tested. The inhibitory activity is quantified in vitro in appropriate cell culture models and for respiratory viral pathogens (respiratory syncytial virus and SARS-CoV-2) in mice. Results of this study comprise a significant step along the translational path of macromolecular inhibitors of virus cell entry, specifically against enveloped respiratory viruses.
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Affiliation(s)
- Rüdiger Groß
- Institute of Molecular VirologyUlm University Medical CenterUlm89081Germany
| | - Lívia Mesquita Dias Loiola
- Department of Chemistry and iNano Interdisciplinary Nanoscience CentreAarhus UniversityAarhus8000Denmark
- Brazilian Synchrotron Light LaboratoryBrazilian Center for Research in Energy and MaterialsCampinasSão Paulo13083‐970Brazil
| | - Leila Issmail
- Fraunhofer Institute for Cell Therapy and Immunology IZILeipzig04103Germany
| | - Nadja Uhlig
- Fraunhofer Institute for Cell Therapy and Immunology IZILeipzig04103Germany
| | - Valentina Eberlein
- Fraunhofer Institute for Cell Therapy and Immunology IZILeipzig04103Germany
| | - Carina Conzelmann
- Institute of Molecular VirologyUlm University Medical CenterUlm89081Germany
| | - Lia‐Raluca Olari
- Institute of Molecular VirologyUlm University Medical CenterUlm89081Germany
| | - Lena Rauch
- Institute of Molecular VirologyUlm University Medical CenterUlm89081Germany
| | - Jan Lawrenz
- Institute of Molecular VirologyUlm University Medical CenterUlm89081Germany
| | - Tatjana Weil
- Institute of Molecular VirologyUlm University Medical CenterUlm89081Germany
| | - Janis A. Müller
- Institute of Molecular VirologyUlm University Medical CenterUlm89081Germany
| | - Mateus Borba Cardoso
- Brazilian Synchrotron Light LaboratoryBrazilian Center for Research in Energy and MaterialsCampinasSão Paulo13083‐970Brazil
| | - Andrea Gilg
- Institute of Molecular VirologyUlm University Medical CenterUlm89081Germany
| | | | | | - Sandra Axberg Pålsson
- Department of Molecular BiosciencesThe Wenner‐Gren Institute Stockholm UniversityStockholm10691Sweden
| | - Anna Selch Tvilum
- Department of Chemistry and iNano Interdisciplinary Nanoscience CentreAarhus UniversityAarhus8000Denmark
| | - Kaja Borup Løvschall
- Department of Chemistry and iNano Interdisciplinary Nanoscience CentreAarhus UniversityAarhus8000Denmark
| | - Maria M. Kristensen
- Department of Chemistry and iNano Interdisciplinary Nanoscience CentreAarhus UniversityAarhus8000Denmark
| | - Anna‐Lena Spetz
- Department of Molecular BiosciencesThe Wenner‐Gren Institute Stockholm UniversityStockholm10691Sweden
| | | | - Marie Galloux
- Université Paris‐SaclayINRAE, UVSQ, VIMJouy‐en‐Josas78352France
| | - Thomas Grunwald
- Fraunhofer Institute for Cell Therapy and Immunology IZILeipzig04103Germany
| | - Alexander N. Zelikin
- Department of Chemistry and iNano Interdisciplinary Nanoscience CentreAarhus UniversityAarhus8000Denmark
| | - Jan Münch
- Institute of Molecular VirologyUlm University Medical CenterUlm89081Germany
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40
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Fujioka Y, Kashiwagi S, Yoshida A, Satoh AO, Fujioka M, Amano M, Yamauchi Y, Ohba Y. A method for the generation of pseudovirus particles bearing SARS coronavirus spike protein in high yields. Cell Struct Funct 2022; 47:43-53. [PMID: 35491102 PMCID: PMC10511058 DOI: 10.1247/csf.21047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 04/19/2022] [Indexed: 12/17/2023] Open
Abstract
The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has threatened human health and the global economy. Development of additional vaccines and therapeutics is urgently required, but such development with live virus must be conducted with biosafety level 3 confinement. Pseudotyped viruses have been widely adopted for studies of virus entry and pharmaceutical development to overcome this restriction. Here we describe a modified protocol to generate vesicular stomatitis virus (VSV) pseudotyped with SARS-CoV or SARS-CoV-2 spike protein in high yield. We found that a large proportion of pseudovirions produced with the conventional transient expression system lacked coronavirus spike protein at their surface as a result of inhibition of parental VSV infection by overexpression of this protein. Establishment of stable cell lines with an optimal expression level of coronavirus spike protein allowed the efficient production of progeny pseudoviruses decorated with spike protein. This improved VSV pseudovirus production method should facilitate studies of coronavirus entry and development of antiviral agents.Key words: severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, pseudovirus, vesicular stomatitis virus (VSV), spike protein.
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Affiliation(s)
- Yoichiro Fujioka
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, N12W6, Kita-ku, Sapporo 060-8612, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
| | - Sayaka Kashiwagi
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, N12W6, Kita-ku, Sapporo 060-8612, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
| | - Aiko Yoshida
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, N12W6, Kita-ku, Sapporo 060-8612, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
| | - Aya O. Satoh
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
| | - Mari Fujioka
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
| | - Maho Amano
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
| | - Yohei Yamauchi
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Yusuke Ohba
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, N12W6, Kita-ku, Sapporo 060-8612, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
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41
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Quandt J, Muik A, Salisch N, Lui BG, Lutz S, Krüger K, Wallisch AK, Adams-Quack P, Bacher M, Finlayson A, Ozhelvaci O, Vogler I, Grikscheit K, Hoehl S, Goetsch U, Ciesek S, Türeci Ö, Sahin U. Omicron BA.1 breakthrough infection drives cross-variant neutralization and memory B cell formation against conserved epitopes. Sci Immunol 2022; 7:eabq2427. [PMID: 35653438 PMCID: PMC9162083 DOI: 10.1126/sciimmunol.abq2427] [Citation(s) in RCA: 112] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Omicron is the evolutionarily most distinct SARS-CoV-2 variant of concern (VOC) to date. We report that Omicron BA.1 breakthrough infection in BNT162b2-vaccinated individuals resulted in strong neutralizing activity against Omicron BA.1, BA.2 and previous SARS-CoV-2 VOCs, but not against the Omicron sublineages BA.4 and BA.5. BA.1 breakthrough infection induced a robust recall response, primarily expanding BMEM cells against epitopes shared broadly amongst variants, rather than inducing BA.1-specific B cells. The vaccination-imprinted BMEM cell pool had sufficient plasticity to be remodeled by heterologous SARS-CoV-2 spike glycoprotein exposure. While selective amplification of BMEM cells recognizing shared epitopes allows for effective neutralization of most variants that evade previously established immunity, susceptibility to escape by variants that acquire alterations at hitherto conserved sites may be heightened.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Maren Bacher
- BioNTech, An der Goldgrube 12, 55131 Mainz, Germany
| | | | | | | | - Katharina Grikscheit
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Sebastian Hoehl
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Udo Goetsch
- Health Protection Authority, City of Frankfurt, 60313 Frankfurt, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany.,DZIF - German Centre for Infection Research, External Partner Site, 60596 Frankfurt, Germany
| | - Özlem Türeci
- BioNTech, An der Goldgrube 12, 55131 Mainz, Germany.,HI-TRON - Helmholtz Institute for Translational Oncology Mainz by DKFZ, Obere Zahlbacherstr. 63, 55131 Mainz, Germany
| | - Ugur Sahin
- BioNTech, An der Goldgrube 12, 55131 Mainz, Germany.,TRON gGmbH - Translational Oncology at the University Medical Center of the Johannes Gutenberg, University Freiligrathstraße 12, 55131 Mainz, Germany
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42
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Arora P, Zhang L, Krüger N, Rocha C, Sidarovich A, Schulz S, Kempf A, Graichen L, Moldenhauer AS, Cossmann A, Dopfer-Jablonka A, Behrens GMN, Jäck HM, Pöhlmann S, Hoffmann M. SARS-CoV-2 Omicron sublineages show comparable cell entry but differential neutralization by therapeutic antibodies. Cell Host Microbe 2022; 30:1103-1111.e6. [PMID: 35588741 PMCID: PMC9072809 DOI: 10.1016/j.chom.2022.04.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/20/2022] [Accepted: 04/29/2022] [Indexed: 12/25/2022]
Abstract
The Omicron variant of SARS-CoV-2 evades antibody-mediated neutralization with unprecedented efficiency. At least three Omicron sublineages have been identified—BA.1, BA.2, and BA.3—and BA.2 exhibits increased transmissibility. However, it is currently unknown whether BA.2 differs from the other sublineages regarding cell entry and antibody-mediated inhibition. Here, we show that BA.1, BA.2, and BA.3 enter and fuse target cells with similar efficiency and in an ACE2-dependent manner. However, BA.2 was not efficiently neutralized by seven of eight antibodies used for COVID-19 therapy, including Sotrovimab, which robustly neutralized BA.1. In contrast, BA.2 and BA.3 (but not BA.1) were appreciably neutralized by Cilgavimab, which could constitute a treatment option. Finally, all sublineages were comparably and efficiently neutralized by antibodies induced by BNT162b2 booster vaccination after previous two-dose homologous or heterologous vaccination. Collectively, the Omicron sublineages show comparable cell entry and neutralization by vaccine-induced antibodies but differ in susceptibility to therapeutic antibodies.
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Affiliation(s)
- Prerna Arora
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073 Göttingen, Germany
| | - Lu Zhang
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073 Göttingen, Germany
| | - Nadine Krüger
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | - Cheila Rocha
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073 Göttingen, Germany
| | - Anzhalika Sidarovich
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073 Göttingen, Germany
| | - Sebastian Schulz
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, Glückstraße 6, 91054 Erlangen, Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073 Göttingen, Germany
| | - Luise Graichen
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073 Göttingen, Germany
| | | | - Anne Cossmann
- Department for Rheumatology and Immunology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Alexandra Dopfer-Jablonka
- Department for Rheumatology and Immunology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany; German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstraße 7, 38124 Braunschweig, Germany; Centre for Individualised Infection Medicine (CiiM), Feodor-Lynen-Straße 7, 30625 Hannover, Germany
| | - Georg M N Behrens
- Department for Rheumatology and Immunology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany; German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstraße 7, 38124 Braunschweig, Germany; Centre for Individualised Infection Medicine (CiiM), Feodor-Lynen-Straße 7, 30625 Hannover, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, Glückstraße 6, 91054 Erlangen, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073 Göttingen, Germany.
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073 Göttingen, Germany.
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43
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Caputo I, Caroccia B, Frasson I, Poggio E, Zamberlan S, Morpurgo M, Seccia TM, Calì T, Brini M, Richter SN, Rossi GP. Angiotensin II Promotes SARS-CoV-2 Infection via Upregulation of ACE2 in Human Bronchial Cells. Int J Mol Sci 2022; 23:ijms23095125. [PMID: 35563515 PMCID: PMC9102833 DOI: 10.3390/ijms23095125] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 12/15/2022] Open
Abstract
Blockers of the renin-angiotensin system (RAS) have been reported to increase the angiotensin converting enzyme (ACE)2, the cellular receptor of SARS-CoV-2, and thus the risk and course of COVID-19. Therefore, we investigated if angiotensin (Ang) II and RAS blockers affected ACE2 expression and SARS-CoV-2 infectivity in human epithelial bronchial Calu-3 cells. By infectivity and spike-mediated cell–cell fusion assays, we showed that Ang II acting on the angiotensin type 1 receptor markedly increased ACE2 at mRNA and protein levels, resulting in enhanced SARS-CoV-2 cell entry. These effects were abolished by irbesartan and not affected by the blockade of ACE-1-mediated Ang II formation with ramipril, and of ACE2- mediated Ang II conversion into Ang 1-7 with MLN-4760. Thus, enhanced Ang II production in patients with an activated RAS might expose to a greater spread of COVID-19 infection in lung cells. The protective action of Angiotensin type 1 receptor antagonists (ARBs) documented in these studies provides a mechanistic explanation for the lack of worse outcomes in high-risk COVID-19 patients on RAS blockers.
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Affiliation(s)
- Ilaria Caputo
- Specialized Center for Blood Pressure Disorders-Regione Veneto and Internal Emergency Medicine Unit, Department of Medicine-DIMED, University of Padua, 35128 Padua, Italy; (I.C.); (B.C.); (S.Z.); (T.M.S.)
| | - Brasilina Caroccia
- Specialized Center for Blood Pressure Disorders-Regione Veneto and Internal Emergency Medicine Unit, Department of Medicine-DIMED, University of Padua, 35128 Padua, Italy; (I.C.); (B.C.); (S.Z.); (T.M.S.)
| | - Ilaria Frasson
- Department of Molecular Medicine-DMM, University of Padua, 35121 Padua, Italy; (I.F.); (S.N.R.)
| | - Elena Poggio
- Department of Biology, University of Padua, 35131 Padua, Italy; (E.P.); (M.B.)
| | - Stefania Zamberlan
- Specialized Center for Blood Pressure Disorders-Regione Veneto and Internal Emergency Medicine Unit, Department of Medicine-DIMED, University of Padua, 35128 Padua, Italy; (I.C.); (B.C.); (S.Z.); (T.M.S.)
| | - Margherita Morpurgo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, 35131 Padua, Italy;
| | - Teresa M. Seccia
- Specialized Center for Blood Pressure Disorders-Regione Veneto and Internal Emergency Medicine Unit, Department of Medicine-DIMED, University of Padua, 35128 Padua, Italy; (I.C.); (B.C.); (S.Z.); (T.M.S.)
| | - Tito Calì
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy;
| | - Marisa Brini
- Department of Biology, University of Padua, 35131 Padua, Italy; (E.P.); (M.B.)
| | - Sara N. Richter
- Department of Molecular Medicine-DMM, University of Padua, 35121 Padua, Italy; (I.F.); (S.N.R.)
| | - Gian Paolo Rossi
- Specialized Center for Blood Pressure Disorders-Regione Veneto and Internal Emergency Medicine Unit, Department of Medicine-DIMED, University of Padua, 35128 Padua, Italy; (I.C.); (B.C.); (S.Z.); (T.M.S.)
- Correspondence:
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44
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SARS-CoV-2 variants C.1.2 and B.1.621 (Mu) partially evade neutralization by antibodies elicited upon infection or vaccination. Cell Rep 2022; 39:110754. [PMID: 35477025 PMCID: PMC9010234 DOI: 10.1016/j.celrep.2022.110754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 03/09/2022] [Accepted: 04/07/2022] [Indexed: 12/03/2022] Open
Abstract
Rapid spread of SARS-CoV-2 variants C.1.2 and B.1.621 (Mu variant) in Africa and the Americas, respectively, as well as a high number of mutations in the viral spike proteins raised concerns that these variants might pose an elevated threat to human health. Here, we show that C.1.2 and B.1.621 spike proteins mediate increased entry into certain cell lines but do not exhibit increased ACE2 binding. Further, we demonstrate that C.1.2 and B.1.621 are resistant to neutralization by bamlanivimab but remain sensitive to inhibition by antibody cocktails used for COVID-19 therapy. Finally, we show that C.1.2 and B.1.621 partially escape neutralization by antibodies induced upon infection and vaccination, with escape of vaccine-induced antibodies being as potent as that measured for B.1.351 (Beta variant), which is known to be highly neutralization resistant. Collectively, C.1.2 and B.1.621 partially evade control by vaccine-induced antibodies, suggesting that close monitoring of these variants is warranted.
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45
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Walter JD, Scherer M, Hutter CAJ, Garaeva AA, Zimmermann I, Wyss M, Rheinberger J, Ruedin Y, Earp JC, Egloff P, Sorgenfrei M, Hürlimann LM, Gonda I, Meier G, Remm S, Thavarasah S, van Geest G, Bruggmann R, Zimmer G, Slotboom DJ, Paulino C, Plattet P, Seeger MA. Biparatopic sybodies neutralize SARS-CoV-2 variants of concern and mitigate drug resistance. EMBO Rep 2022; 23:e54199. [PMID: 35253970 PMCID: PMC8982573 DOI: 10.15252/embr.202154199] [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] [Received: 10/21/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 12/15/2022] Open
Abstract
The ongoing COVID‐19 pandemic represents an unprecedented global health crisis. Here, we report the identification of a synthetic nanobody (sybody) pair, Sb#15 and Sb#68, that can bind simultaneously to the SARS‐CoV‐2 spike RBD and efficiently neutralize pseudotyped and live viruses by interfering with ACE2 interaction. Cryo‐EM confirms that Sb#15 and Sb#68 engage two spatially discrete epitopes, influencing rational design of bispecific and tri‐bispecific fusion constructs that exhibit up to 100‐ and 1,000‐fold increase in neutralization potency, respectively. Cryo‐EM of the sybody‐spike complex additionally reveals a novel up‐out RBD conformation. While resistant viruses emerge rapidly in the presence of single binders, no escape variants are observed in the presence of the bispecific sybody. The multivalent bispecific constructs further increase the neutralization potency against globally circulating SARS‐CoV‐2 variants of concern. Our study illustrates the power of multivalency and biparatopic nanobody fusions for the potential development of therapeutic strategies that mitigate the emergence of new SARS‐CoV‐2 escape mutants.
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Affiliation(s)
- Justin D Walter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Melanie Scherer
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Cedric A J Hutter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Alisa A Garaeva
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Department of Membrane Enzymology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Iwan Zimmermann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Linkster Therapeutics AG, Zurich, Switzerland
| | - Marianne Wyss
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jan Rheinberger
- Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Yelena Ruedin
- Institute of Virology and Immunology, Bern & Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jennifer C Earp
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Pascal Egloff
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Linkster Therapeutics AG, Zurich, Switzerland
| | - Michèle Sorgenfrei
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Lea M Hürlimann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Imre Gonda
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Gianmarco Meier
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Sille Remm
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Sujani Thavarasah
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Geert van Geest
- Interfaculty Bioinformatics Unit and Swiss, Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss, Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Gert Zimmer
- Institute of Virology and Immunology, Bern & Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Dirk J Slotboom
- Department of Membrane Enzymology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Cristina Paulino
- Department of Membrane Enzymology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.,Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Philippe Plattet
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
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46
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Puckette M, Barrera J, Schwarz M, Rasmussen M. Method for quantification of porcine type I interferon activity using luminescence, by direct and indirect means. BMC Biotechnol 2022; 22:13. [PMID: 35351081 PMCID: PMC8966355 DOI: 10.1186/s12896-022-00743-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 03/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Type I interferons are widely used in research applications and as biotherapeutics. Current assays used to measure interferon concentrations, such as plaque reduction assays and ELISA, are expensive, technically challenging, and may take days to provide results. We sought to develop a robust and rapid assay to determine interferon concentrations produced from transiently transfected cell cultures. METHOD Indirect quantification of recombinant interferon was evaluated using a novel bi-cistronic construct encoding the Foot-and-mouth disease virus 2A translational interrupter sequence to yield equimolar expression of Gaussia princeps luciferase and porcine interferon α. Direct quantification was evaluated by expression of a novel fusion protein comprised of Gaussia princeps luciferase and porcine type I interferon. Plasmids encoding constructs are transiently transfected into cell cultures and supernatant harvested for testing of luminescence, ELISA determined concentration, and anti-viral activity against vesicular stomatitis virus. RESULTS Bi-cistronic constructs, utilized for indirect quantification, demonstrate both luciferase activity and anti-viral activity. Fusion proteins, utilized for direct quantification, retained secretion and luminescence however only the interferon α fusion protein had antiviral activity comparable to wildtype porcine interferon α. A strong linear correlation was observed between dilution and luminescence for all compounds over a dynamic range of concentrations. CONCLUSION The correlation of antiviral and luciferase activities demonstrated the utility of this approach, both direct and indirect, to rapidly determine recombinant interferon concentrations. Concentration can be determined over a more dynamic concentration range than available ELISA based assays using this methodology.
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Affiliation(s)
- Michael Puckette
- Plum Island Animal Disease Center, U. S. Department of Homeland Security Science and Technology Directorate, P.O. Box 848, Greenport, NY, 11944, USA.
| | - J Barrera
- Plum Island Animal Disease Center, Leidos, Inc., P.O. Box 848, Greenport, NY, 11944, USA
| | - M Schwarz
- Oak Ridge Institute for Science and Education, Plum Island Animal Disease Center Research Participation Program, P.O. Box 848, Greenport, NY, 11944, USA
| | - M Rasmussen
- Plum Island Animal Disease Center, U. S. Department of Homeland Security Science and Technology Directorate, P.O. Box 848, Greenport, NY, 11944, USA
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47
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Arora P, Sidarovich A, Graichen L, Hörnich B, Hahn A, Hoffmann M, Pöhlmann S. Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. PLoS One 2022; 17:e0265453. [PMID: 35333910 PMCID: PMC8956166 DOI: 10.1371/journal.pone.0265453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/01/2022] [Indexed: 01/12/2023] Open
Abstract
Several SARS-CoV-2 variants emerged that harbor mutations in the surface unit of the viral spike (S) protein that enhance infectivity and transmissibility. Here, we analyzed whether ten naturally-occurring mutations found within the extended loop harboring the S1/S2 cleavage site of the S protein, a determinant of SARS-CoV-2 cell tropism and pathogenicity, impact S protein processing and function. None of the mutations increased but several decreased S protein cleavage at the S1/S2 site, including S686G and P681H, the latter of which is found in variants of concern B.1.1.7 (Alpha variant) and B.1.1.529 (Omicron variant). None of the mutations reduced ACE2 binding and cell-cell fusion although several modulated the efficiency of host cell entry. The effects of mutation S686G on viral entry were cell-type dependent and could be linked to the availability of cathepsin L for S protein activation. These results show that polymorphisms at the S1/S2 site can modulate S protein processing and host cell entry.
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Affiliation(s)
- Prerna Arora
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Anzhalika Sidarovich
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Luise Graichen
- Infection Biology Unit, German Primate Center, Göttingen, Germany
| | - Bojan Hörnich
- Junior Research Group Herpesviruses - Infection Biology Unit, German Primate Center, Göttingen, Germany
| | - Alexander Hahn
- Junior Research Group Herpesviruses - Infection Biology Unit, German Primate Center, Göttingen, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
- * E-mail: (MH); (SP)
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
- * E-mail: (MH); (SP)
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48
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Urlaub D, Wolfsdorff N, Hoffmann JE, Dorok S, Hoffmann M, Anft M, Pieris N, Günther P, Schaaf B, Cassens U, Bröde P, Claus M, Picard LK, Wingert S, Backes S, Durak D, Babel N, Pöhlmann S, Renken F, Raunser S, Watzl C. Neutralizing antibody responses 300 days after SARS-CoV-2 infection and induction of high antibody titers after vaccination. Eur J Immunol 2022; 52:810-815. [PMID: 35247269 PMCID: PMC9087412 DOI: 10.1002/eji.202149758] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/27/2022] [Accepted: 03/02/2022] [Indexed: 11/09/2022]
Abstract
Neutralizing antibodies against SARS‐CoV‐2 are important to protect against infection and/or disease. Using an assay to detect antibodies directed against the receptor binding domain (RBD) of SARS‐CoV‐2 Spike, we identified individuals with SARS‐CoV‐2 infection after an outbreak at a local health institution. All but one COVID‐19 patient developed detectable anti‐RBD antibodies and 77% had virus neutralizing antibody titers of >1:25. Antibody levels declined slightly over time. However, we still detected virus neutralizing antibody titers in 64% of the COVID‐19 patients at >300 days after infection, demonstrating durability of neutralizing antibody levels after infection. Importantly, full COVID‐19 vaccination of these individuals resulted in higher antibody titers compared to fully vaccinated individuals in the absence of prior infection. These data demonstrate long‐lived antibody‐mediated immunity after SARS‐CoV‐2 infection, and a clear benefit of two vaccine doses for recovered individuals.
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Affiliation(s)
- Doris Urlaub
- Department for Immunology, Leibniz Research Centre for Working Environment and Human Factors (IfADo) at TU Dortmund, Dortmund, Germany
| | - Natalie Wolfsdorff
- Department for Immunology, Leibniz Research Centre for Working Environment and Human Factors (IfADo) at TU Dortmund, Dortmund, Germany
| | - Jan-Erik Hoffmann
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Stefanie Dorok
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany.,Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Moritz Anft
- Center for Translational Medicine and Immune Diagnostics Laboratory, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany
| | - Naomi Pieris
- Department for Immunology, Leibniz Research Centre for Working Environment and Human Factors (IfADo) at TU Dortmund, Dortmund, Germany
| | - Patrick Günther
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Bernhard Schaaf
- Department of Respiratory Medicine and Infectious Diseases, Klinikum Dortmund, Dortmund, Germany.,Faculty of Health, University Witten/Herdecke, Herdecke, Germany
| | - Uwe Cassens
- Institute for Transfusion Medicine, Laboratory Medicine and Medical Microbiology, Medical Center Dortmund, Dortmund, Germany
| | - Peter Bröde
- Department for Immunology, Leibniz Research Centre for Working Environment and Human Factors (IfADo) at TU Dortmund, Dortmund, Germany
| | - Maren Claus
- Department for Immunology, Leibniz Research Centre for Working Environment and Human Factors (IfADo) at TU Dortmund, Dortmund, Germany
| | - Lea K Picard
- Department for Immunology, Leibniz Research Centre for Working Environment and Human Factors (IfADo) at TU Dortmund, Dortmund, Germany
| | - Sabine Wingert
- Department for Immunology, Leibniz Research Centre for Working Environment and Human Factors (IfADo) at TU Dortmund, Dortmund, Germany
| | - Simone Backes
- Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany
| | - Deniz Durak
- Dortmund Health Department, Dortmund, Germany
| | - Nina Babel
- Center for Translational Medicine and Immune Diagnostics Laboratory, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany.,Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | | | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Carsten Watzl
- Department for Immunology, Leibniz Research Centre for Working Environment and Human Factors (IfADo) at TU Dortmund, Dortmund, Germany
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49
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Van Ert HA, Bohan DW, Rogers K, Fili M, Rojas Chávez RA, Qing E, Han C, Dempewolf S, Hu G, Schwery N, Sevcik K, Ruggio N, Boyt D, Pentella MA, Gallagher T, Jackson JB, Merrill AE, Knudson CM, Brown GD, Maury W, Haim H. Limited Variation between SARS-CoV-2-Infected Individuals in Domain Specificity and Relative Potency of the Antibody Response against the Spike Glycoprotein. Microbiol Spectr 2022; 10:e0267621. [PMID: 35080430 PMCID: PMC8791189 DOI: 10.1128/spectrum.02676-21] [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: 12/21/2021] [Accepted: 12/28/2021] [Indexed: 11/25/2022] Open
Abstract
The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is arranged as a trimer on the virus surface, composed of three S1 and three S2 subunits. Infected and vaccinated individuals generate antibodies against spike, which can neutralize the virus. Most antibodies target the receptor-binding domain (RBD) and N-terminal domain (NTD) of S1; however, antibodies against other regions of spike have also been isolated. The interhost variability in domain specificity and relative neutralization efficacy of the antibodies is still poorly characterized. To this end, we tested serum and plasma samples collected from 85 coronavirus disease 2019 (COVID-19) convalescent subjects. Samples were analyzed using seven immunoassays that employ different domains, subunits, and oligomeric forms of spike to capture the antibodies. Samples were also tested for their neutralization of pseudovirus containing SARS-CoV-2 spike and of replication-competent SARS-CoV-2. While the total amount of anti-spike antibodies produced varied among convalescent subjects, we observed an unexpectedly fixed ratio of RBD- to NTD-targeting antibodies. The relative potency of the response (defined as the measured neutralization efficacy relative to the total level of spike-targeting antibodies) also exhibited limited variation between subjects and was not associated with the overall amount of antispike antibodies produced. These studies suggest that host-to-host variation in the polyclonal response elicited against SARS-CoV-2 spike in early pandemic subjects is primarily limited to the quantity of antibodies generated rather than their domain specificity or relative neutralization potency. IMPORTANCE Infection by SARS-CoV-2 elicits antibodies against various domains of the spike protein, including the RBD and NTD of subunit S1 and against subunit S2. The antibody responses of different infected individuals exhibit different efficacies to inactivate (neutralize) the virus. Here, we show that the observed variation in the neutralizing activity of the antibody responses in COVID-19 convalescent subjects is caused by differences in the amounts of antibodies rather than their recognition properties or the potency of their antiviral activity. These findings suggest that COVID-19 vaccine strategies that focus on enhancing the overall level of the antibodies will likely elicit a more uniformly efficacious protective response.
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Affiliation(s)
- Hanora A. Van Ert
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Dana W. Bohan
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Kai Rogers
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Mohammad Fili
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, Iowa, United States
| | - Roberth A. Rojas Chávez
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Enya Qing
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, United States
| | - Changze Han
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Spencer Dempewolf
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Guiping Hu
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, Iowa, United States
| | - Nathan Schwery
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Kristina Sevcik
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Natalie Ruggio
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Devlin Boyt
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Michael A. Pentella
- State Hygienic Laboratory, The University of Iowa, Iowa City, Iowa, United States
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, United States
| | - J. Brooks Jackson
- Department of Pathology, University of Iowa Hospitals & Clinics, Iowa City, Iowa, United States
| | - Anna E. Merrill
- Department of Pathology, University of Iowa Hospitals & Clinics, Iowa City, Iowa, United States
| | - C. Michael Knudson
- Department of Pathology, University of Iowa Hospitals & Clinics, Iowa City, Iowa, United States
| | - Grant D. Brown
- Department of Biostatistics, School of Public Health, The University of Iowa, Iowa City, Iowa, United States
| | - Wendy Maury
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Hillel Haim
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
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50
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Batista AD, Rajpal S, Keitel B, Dietl S, Fresco‐Cala B, Dinc M, Groß R, Sobek H, Münch J, Mizaikoff B. Plastic Antibodies Mimicking the ACE2 Receptor for Selective Binding of SARS-CoV-2 Spike. ADVANCED MATERIALS INTERFACES 2022; 9:2101925. [PMID: 35441074 PMCID: PMC9011513 DOI: 10.1002/admi.202101925] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/16/2021] [Indexed: 06/14/2023]
Abstract
Molecular imprinting has proven to be a versatile and simple strategy to obtain selective materials also termed "plastic antibodies" for a wide variety of species, i.e., from ions to macromolecules and viruses. However, to the best of the authors' knowledge, the development of epitope-imprinted polymers for selective binding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not reported to date. An epitope from the SARS-CoV-2 spike protein comprising 17 amino acids is used as a template during the imprinting process. The interactions between the epitope template and organosilane monomers used for the polymer synthesis are predicted via molecular docking simulations. The molecularly imprinted polymer presents a 1.8-fold higher selectivity against the target epitope compared to non-imprinted control polymers. Rebinding studies with pseudoviruses containing SARS-CoV-2 spike protein demonstrate the superior selectivity of the molecularly imprinted matrices, which mimic the interactions of angiotensin-converting enzyme 2 receptors from human cells. The obtained results highlight the potential of SARS-CoV-2 molecularly imprinted polymers for a variety of applications including chem/biosensing and antiviral delivery.
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Affiliation(s)
- Alex D. Batista
- Institute of Analytical and Bioanalytical ChemistryUlm UniversityAlbert‐Einstein‐Allee 1189081UlmGermany
- Institute of ChemistryFederal University of UberlandiaAv. Joao Naves de Ávila 2121Uberlândia38400‐902Brazil
| | - Soumya Rajpal
- Institute of Analytical and Bioanalytical ChemistryUlm UniversityAlbert‐Einstein‐Allee 1189081UlmGermany
- Department of Biochemical Engineering and BiotechnologyIndian Institute of Technology DelhiHauz KhasNew Delhi110 016India
| | - Benedikt Keitel
- Institute of Analytical and Bioanalytical ChemistryUlm UniversityAlbert‐Einstein‐Allee 1189081UlmGermany
| | - Sandra Dietl
- Institute of Analytical and Bioanalytical ChemistryUlm UniversityAlbert‐Einstein‐Allee 1189081UlmGermany
| | - Beatriz Fresco‐Cala
- Institute of Analytical and Bioanalytical ChemistryUlm UniversityAlbert‐Einstein‐Allee 1189081UlmGermany
| | | | - Rüdiger Groß
- Institute of Molecular VirologyUlm University Medical CenterMeyerhofstr. 189081UlmGermany
| | - Harald Sobek
- Labor Dr. Merk & Kollegen GmbHBeim Braunland 188416OchsenhausenGermany
| | - Jan Münch
- Institute of Molecular VirologyUlm University Medical CenterMeyerhofstr. 189081UlmGermany
| | - Boris Mizaikoff
- Institute of Analytical and Bioanalytical ChemistryUlm UniversityAlbert‐Einstein‐Allee 1189081UlmGermany
- Hahn‐SchickardSedanstraße 1489077UlmGermany
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