1
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Guo H, Cho B, Hinton PR, He S, Yu Y, Ramesh AK, Sivaccumar JP, Ku Z, Campo K, Holland S, Sachdeva S, Mensch C, Dawod M, Whitaker A, Eisenhauer P, Falcone A, Honce R, Botten JW, Carroll SF, Keyt BA, Womack AW, Strohl WR, Xu K, Zhang N, An Z, Ha S, Shiver JW, Fu TM. An ACE2 decamer viral trap as a durable intervention solution for current and future SARS-CoV. Emerg Microbes Infect 2023; 12:2275598. [PMID: 38078382 PMCID: PMC10768737 DOI: 10.1080/22221751.2023.2275598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/19/2023] [Indexed: 12/18/2023]
Abstract
The capacity of SARS-CoV-2 to evolve poses challenges to conventional prevention and treatment options such as vaccination and monoclonal antibodies, as they rely on viral receptor binding domain (RBD) sequences from previous strains. Additionally, animal CoVs, especially those of the SARS family, are now appreciated as a constant pandemic threat. We present here a new antiviral approach featuring inhalation delivery of a recombinant viral trap composed of ten copies of angiotensin-converting enzyme 2 (ACE2) fused to the IgM Fc. This ACE2 decamer viral trap is designed to inhibit SARS-CoV-2 entry function, regardless of viral RBD sequence variations as shown by its high neutralization potency against all known SARS-CoV-2 variants, including Omicron BQ.1, BQ.1.1, XBB.1 and XBB.1.5. In addition, it demonstrates potency against SARS-CoV-1, human NL63, as well as bat and pangolin CoVs. The multivalent trap is effective in both prophylactic and therapeutic settings since a single intranasal dosing confers protection in human ACE2 transgenic mice against viral challenges. Lastly, this molecule is stable at ambient temperature for more than twelve weeks and can sustain physical stress from aerosolization. These results demonstrate the potential of a decameric ACE2 viral trap as an inhalation solution for ACE2-dependent coronaviruses of current and future pandemic concerns.
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Affiliation(s)
| | | | | | - Sijia He
- IGM Biosciences, Mountain View, CA, USA
| | | | - Ashwin Kumar Ramesh
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jwala Priyadarsini Sivaccumar
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | | | | | | | | | - Annalis Whitaker
- Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT, USA
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, University of Vermont, Burlington, VT, USA
| | - Philip Eisenhauer
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, University of Vermont, Burlington, VT, USA
| | - Allison Falcone
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, University of Vermont, Burlington, VT, USA
| | - Rebekah Honce
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, University of Vermont, Burlington, VT, USA
| | - Jason W. Botten
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, University of Vermont, Burlington, VT, USA
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, USA
| | | | | | | | | | - Kai Xu
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Ningyan Zhang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Sha Ha
- IGM Biosciences, Mountain View, CA, USA
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2
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Shrestha L, Lin MJ, Xie H, Mills MG, Mohamed Bakhash SA, Gaur VP, Livingston RJ, Castor J, Bruce EA, Botten JW, Huang ML, Jerome KR, Greninger AL, Roychoudhury P. Clinical performance characteristics of the Swift Normalase Amplicon Panel for sensitive recovery of SARS-CoV-2 genomes. J Mol Diagn 2022; 24:963-976. [PMID: 35863699 PMCID: PMC9290336 DOI: 10.1016/j.jmoldx.2022.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/24/2022] [Accepted: 05/27/2022] [Indexed: 11/18/2022] Open
Abstract
Amplicon-based sequencing methods are central in characterizing the diversity, transmission, and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but need to be rigorously assessed for clinical utility. Herein, we validated the Swift Biosciences' SARS-CoV-2 Swift Normalase Amplicon Panels using remnant clinical specimens. High-quality genomes meeting our established library and sequence quality criteria were recovered from positive specimens, with 95% limit of detection of 40.08 SARS-CoV-2 copies/PCR. Breadth of genome recovery was evaluated across a range of CT values (11.3 to 36.7; median, 21.6). Of 428 positive samples, 413 (96.5%) generated genomes with <10% unknown bases, with a mean genome coverage of 13,545× ± SD 8382×. No genomes were recovered from PCR-negative specimens (n = 30) or from specimens positive for non–SARS-CoV-2 respiratory viruses (n = 20). Compared with whole-genome shotgun metagenomic sequencing (n = 14) or Sanger sequencing for the spike gene (n = 11), pairwise identity between consensus sequences was 100% in all cases, with highly concordant allele frequencies (R2 = 0.99) between Swift and shotgun libraries. When samples from different clades were mixed at varying ratios, expected variants were detected even in 1:99 mixtures. When deployed as a clinical test, 268 tests were performed in the first 23 weeks, with a median turnaround time of 11 days, ordered primarily for outbreak investigations and infection control.
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Affiliation(s)
- Lasata Shrestha
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Michelle J Lin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Margaret G Mills
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | | | - Vinod P Gaur
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Robert J Livingston
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Jared Castor
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Emily A Bruce
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT
| | - Jason W Botten
- Department of Medicine, University of Vermont, Burlington, VT
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Keith R Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA.
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA.
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3
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Bruce EA, Mills MG, Sampoleo R, Perchetti GA, Huang ML, Despres HW, Schmidt MM, Roychoudhury P, Shirley DJ, Jerome KR, Greninger AL, Botten JW. Predicting infectivity: comparing four PCR-based assays to detect culturable SARS-CoV-2 in clinical samples. EMBO Mol Med 2021; 14:e15290. [PMID: 34862752 PMCID: PMC8819313 DOI: 10.15252/emmm.202115290] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 01/04/2023] Open
Abstract
With the COVID‐19 pandemic caused by SARS‐CoV‐2 now in its second year, there remains an urgent need for diagnostic testing that can identify infected individuals, particularly those who harbor infectious virus. Various RT–PCR strategies have been proposed to identify specific viral RNA species that may predict the presence of infectious virus, including detection of transcriptional intermediates (e.g., subgenomic RNA [sgRNA]) and replicative intermediates (e.g., negative‐strand RNA species). Using a novel primer/probe set for detection of subgenomic (sg)E transcripts, we successfully identified 100% of specimens containing culturable SARS‐CoV‐2 from a set of 126 clinical samples (total sgE CT values ranging from 12.3 to 37.5). This assay showed superior performance compared to a previously published sgRNA assay and to a negative‐strand RNA assay, both of which failed to detect target RNA in a subset of samples from which we isolated live virus. In addition, total levels of viral RNA (genome, negative‐strand, and sgE) detected with the WHO/Charité primer‐probe set correlated closely with levels of infectious virus. Specifically, infectious virus was not detected in samples with a CT above 31.0. Clinical samples with higher levels of viral RNA also displayed cytopathic effect (CPE) more quickly than those with lower levels of viral RNA. Finally, we found that the infectivity of SARS‐CoV‐2 samples is significantly dependent on the cell type used for viral isolation, as Vero E6 cells expressing TMRPSS2 extended the analytical sensitivity of isolation by more than 3 CT compared to parental Vero E6 cells and resulted in faster isolation. Our work shows that using a total viral RNA Ct cutoff of > 31 or specifically testing for sgRNA can serve as an effective rule‐out test for the presence of culturable virus.
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Affiliation(s)
- Emily A Bruce
- Division of Immunobiology, Department of Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, USA
| | - Margaret G Mills
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Reigran Sampoleo
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Garrett A Perchetti
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Meei-Li Huang
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Hannah W Despres
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, USA
| | - Madaline M Schmidt
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, USA
| | - Pavitra Roychoudhury
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Keith R Jerome
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alexander L Greninger
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jason W Botten
- Division of Immunobiology, Department of Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, USA.,Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, USA
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4
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Victor J, Deutsch J, Whitaker A, Lamkin EN, March A, Zhou P, Botten JW, Chatterjee N. SARS-CoV-2 triggers DNA damage response in Vero E6 cells. Biochem Biophys Res Commun 2021; 579:141-145. [PMID: 34600299 PMCID: PMC8440005 DOI: 10.1016/j.bbrc.2021.09.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 12/27/2022]
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus responsible for the current COVID-19 pandemic and has now infected more than 200 million people with more than 4 million deaths globally. Recent data suggest that symptoms and general malaise may continue long after the infection has ended in recovered patients, suggesting that SARS-CoV-2 infection has profound consequences in the host cells. Here we report that SARS-CoV-2 infection can trigger a DNA damage response (DDR) in African green monkey kidney cells (Vero E6). We observed a transcriptional upregulation of the Ataxia telangiectasia and Rad3 related protein (ATR) in infected cells. In addition, we observed enhanced phosphorylation of CHK1, a downstream effector of the ATR DNA damage response, as well as H2AX. Strikingly, SARS-CoV-2 infection lowered the expression of TRF2 shelterin-protein complex, and reduced telomere lengths in infected Vero E6 cells. Thus, our observations suggest SARS-CoV-2 may have pathological consequences to host cells beyond evoking an immunopathogenic immune response.
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Affiliation(s)
- Joshua Victor
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Jamie Deutsch
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Annalis Whitaker
- Division of Immunobiology, Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Erica N Lamkin
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Anthony March
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Pei Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Jason W Botten
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA; Division of Immunobiology, Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Nimrat Chatterjee
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA; Division of Immunobiology, Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA; University of Vermont Cancer Center, University of Vermont, Burlington, VT, 05405, USA.
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5
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Rissanen I, Krumm SA, Stass R, Whitaker A, Voss JE, Bruce EA, Rothenberger S, Kunz S, Burton DR, Huiskonen JT, Botten JW, Bowden TA, Doores KJ. Structural Basis for a Neutralizing Antibody Response Elicited by a Recombinant Hantaan Virus Gn Immunogen. mBio 2021; 12:e0253120. [PMID: 34225492 PMCID: PMC8406324 DOI: 10.1128/mbio.02531-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Hantaviruses are a group of emerging pathogens capable of causing severe disease upon zoonotic transmission to humans. The mature hantavirus surface presents higher-order tetrameric assemblies of two glycoproteins, Gn and Gc, which are responsible for negotiating host cell entry and constitute key therapeutic targets. Here, we demonstrate that recombinantly derived Gn from Hantaan virus (HTNV) elicits a neutralizing antibody response (serum dilution that inhibits 50% infection [ID50], 1:200 to 1:850) in an animal model. Using antigen-specific B cell sorting, we isolated monoclonal antibodies (mAbs) exhibiting neutralizing and non-neutralizing activity, termed mAb HTN-Gn1 and mAb nnHTN-Gn2, respectively. Crystallographic analysis reveals that these mAbs target spatially distinct epitopes at disparate sites of the N-terminal region of the HTNV Gn ectodomain. Epitope mapping onto a model of the higher order (Gn-Gc)4 spike supports the immune accessibility of the mAb HTN-Gn1 epitope, a hypothesis confirmed by electron cryo-tomography of the antibody with virus-like particles. These data define natively exposed regions of the hantaviral Gn that can be targeted in immunogen design. IMPORTANCE The spillover of pathogenic hantaviruses from rodent reservoirs into the human population poses a continued threat to human health. Here, we show that a recombinant form of the Hantaan virus (HTNV) surface-displayed glycoprotein, Gn, elicits a neutralizing antibody response in rabbits. We isolated a neutralizing (HTN-Gn1) and a non-neutralizing (nnHTN-Gn2) monoclonal antibody and provide the first molecular-level insights into how the Gn glycoprotein may be targeted by the antibody-mediated immune response. These findings may guide rational vaccine design approaches focused on targeting the hantavirus glycoprotein envelope.
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Affiliation(s)
- Ilona Rissanen
- Division of Structural Biology, Wellcome Centre for Human Genetics, grid.4991.5University of Oxford, Oxford, United Kingdom
- Institute of Biotechnology and Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Stefanie A. Krumm
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Robert Stass
- Division of Structural Biology, Wellcome Centre for Human Genetics, grid.4991.5University of Oxford, Oxford, United Kingdom
| | - Annalis Whitaker
- Division of Immunobiology, Department of Medicine, Larner College of Medicine, grid.59062.38University of Vermont, Burlington, Vermont, USA
- Cellular, Molecular, and Biomedical Sciences Graduate Program, grid.59062.38University of Vermont, Burlington, Vermont, USA
| | - James E. Voss
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Emily A. Bruce
- Division of Immunobiology, Department of Medicine, Larner College of Medicine, grid.59062.38University of Vermont, Burlington, Vermont, USA
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, grid.59062.38University of Vermont, Burlington, Vermont, USA
| | - Sylvia Rothenberger
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Stefan Kunz
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, Massachusetts, USA
| | - Juha T. Huiskonen
- Division of Structural Biology, Wellcome Centre for Human Genetics, grid.4991.5University of Oxford, Oxford, United Kingdom
- Institute of Biotechnology and Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Jason W. Botten
- Division of Immunobiology, Department of Medicine, Larner College of Medicine, grid.59062.38University of Vermont, Burlington, Vermont, USA
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, grid.59062.38University of Vermont, Burlington, Vermont, USA
| | - Thomas A. Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, grid.4991.5University of Oxford, Oxford, United Kingdom
| | - Katie J. Doores
- Department of Infectious Diseases, King's College London, London, United Kingdom
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6
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Drayman N, DeMarco JK, Jones KA, Azizi SA, Froggatt HM, Tan K, Maltseva NI, Chen S, Nicolaescu V, Dvorkin S, Furlong K, Kathayat RS, Firpo MR, Mastrodomenico V, Bruce EA, Schmidt MM, Jedrzejczak R, Muñoz-Alía MÁ, Schuster B, Nair V, Han KY, O’Brien A, Tomatsidou A, Meyer B, Vignuzzi M, Missiakas D, Botten JW, Brooke CB, Lee H, Baker SC, Mounce BC, Heaton NS, Severson WE, Palmer KE, Dickinson BC, Joachimiak A, Randall G, Tay S. Masitinib is a broad coronavirus 3CL inhibitor that blocks replication of SARS-CoV-2. Science 2021; 373:931-936. [PMID: 34285133 PMCID: PMC8809056 DOI: 10.1126/science.abg5827] [Citation(s) in RCA: 152] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 07/14/2021] [Indexed: 01/16/2023]
Abstract
There is an urgent need for antiviral agents that treat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We screened a library of 1900 clinically safe drugs against OC43, a human beta coronavirus that causes the common cold, and evaluated the top hits against SARS-CoV-2. Twenty drugs significantly inhibited replication of both viruses in cultured human cells. Eight of these drugs inhibited the activity of the SARS-CoV-2 main protease, 3CLpro, with the most potent being masitinib, an orally bioavailable tyrosine kinase inhibitor. X-ray crystallography and biochemistry show that masitinib acts as a competitive inhibitor of 3CLpro. Mice infected with SARS-CoV-2 and then treated with masitinib showed >200-fold reduction in viral titers in the lungs and nose, as well as reduced lung inflammation. Masitinib was also effective in vitro against all tested variants of concern (B.1.1.7, B.1.351, and P.1).
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Affiliation(s)
- Nir Drayman
- Pritzker School for Molecular Engineering, The University of Chicago, Chicago, IL, USA.,Corresponding author. (S.T.); (N.D.)
| | - Jennifer K. DeMarco
- Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Krysten A. Jones
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Saara-Anne Azizi
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Heather M. Froggatt
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.,Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
| | - Kemin Tan
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.,Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA.,Department of Medicine, Division of Immunobiology, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Natalia Ivanovna Maltseva
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.,Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA.,Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Siquan Chen
- Cellular Screening Center, The University of Chicago, Chicago, IL, USA.,Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Vlad Nicolaescu
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Steve Dvorkin
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Kevin Furlong
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Rahul S. Kathayat
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Mason R. Firpo
- Pritzker School for Molecular Engineering, The University of Chicago, Chicago, IL, USA.,Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Vincent Mastrodomenico
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Emily A. Bruce
- Cellular Screening Center, The University of Chicago, Chicago, IL, USA.,Department of Medicine, Division of Immunobiology, Larner College of Medicine, University of Vermont, Burlington, VT, USA.,Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Madaline M. Schmidt
- Department of Medicine, Division of Immunobiology, Larner College of Medicine, University of Vermont, Burlington, VT, USA.,Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Robert Jedrzejczak
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.,Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
| | | | - Brooke Schuster
- Pritzker School for Molecular Engineering, The University of Chicago, Chicago, IL, USA.,Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Vishnu Nair
- Pritzker School for Molecular Engineering, The University of Chicago, Chicago, IL, USA.,Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Kyu-yeon Han
- Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA.,Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Amornrat O’Brien
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, Biophysics Core at Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Anastasia Tomatsidou
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA.,Department of Medicine, Division of Immunobiology, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Bjoern Meyer
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
| | - Marco Vignuzzi
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA.,Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
| | - Dominique Missiakas
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Jason W. Botten
- Cellular Screening Center, The University of Chicago, Chicago, IL, USA.,Department of Medicine, Division of Immunobiology, Larner College of Medicine, University of Vermont, Burlington, VT, USA.,Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, USA.,Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Christopher B. Brooke
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hyun Lee
- Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, Biophysics Core at Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Susan C. Baker
- Pritzker School for Molecular Engineering, The University of Chicago, Chicago, IL, USA.,Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.,Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
| | - Bryan C. Mounce
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.,Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Nicholas S. Heaton
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.,Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
| | - William E. Severson
- Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA.,Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Kenneth E. Palmer
- Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Bryan C. Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Andrzej Joachimiak
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.,Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Glenn Randall
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Savaş Tay
- Pritzker School for Molecular Engineering, The University of Chicago, Chicago, IL, USA.,Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA.,Corresponding author. (S.T.); (N.D.)
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7
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Tu HA, Nivarthi UK, Graham NR, Eisenhauer P, Delacruz MJ, Pierce KK, Whitehead SS, Boyson JE, Botten JW, Kirkpatrick BD, Durbin AP, deSilva AM, Diehl SA. Stimulation of B Cell Immunity in Flavivirus-Naive Individuals by the Tetravalent Live Attenuated Dengue Vaccine TV003. Cell Rep Med 2020; 1:100155. [PMID: 33377126 PMCID: PMC7762770 DOI: 10.1016/j.xcrm.2020.100155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 09/09/2020] [Accepted: 11/18/2020] [Indexed: 02/05/2023]
Abstract
The tetravalent live attenuated dengue vaccine candidate TV003 induces neutralizing antibodies against all four dengue virus serotypes (DENV1–DENV4) and protects against experimental challenge with DENV2 in humans. Here, we track vaccine viremia and B and T cell responses to this vaccination/challenge model to understand how vaccine viremia links adaptive immunity and development of protective antibody responses. TV003 viremia triggers an acute plasmablast response that, in combination with DENV-specific CD4+ T cells, correlates with serum neutralizing antibodies. TV003 vaccinees develop DENV2-reactive memory B cells, including serotype-specific and multivalent specificities in line with the composition of serum antibodies. There is no post-challenge plasmablast response in vaccinees, although stronger and earlier post-TV003 plasmablast responses associate with sterile humoral protection from DENV2 challenge. TV003 vaccine triggers plasmablasts and memory B cells, which, with support from CD4+ T cells, functionally link early vaccine viremia and the serum antibody responses. The tetravalent live attenuated dengue vaccine TV003 stimulates plasmablasts Robust plasmablast response is associated with sterile protection from challenge DENV-specific memory B cells persist 6 months after vaccination DENV-specific CD4+ T cells correlate with neutralizing antibodies
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Affiliation(s)
- Huy A Tu
- Department of Microbiology and Molecular Genetics, Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA.,Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT 05405, USA
| | - Usha K Nivarthi
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Nancy R Graham
- Department of Microbiology and Molecular Genetics, Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Philip Eisenhauer
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Matthew J Delacruz
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Kristen K Pierce
- Department of Microbiology and Molecular Genetics, Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA.,Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Stephen S Whitehead
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan E Boyson
- Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT 05405, USA.,Department of Surgery, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Jason W Botten
- Department of Microbiology and Molecular Genetics, Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA.,Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT 05405, USA.,Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Beth D Kirkpatrick
- Department of Microbiology and Molecular Genetics, Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA.,Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Anna P Durbin
- Department of International Health, Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Aravinda M deSilva
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Sean A Diehl
- Department of Microbiology and Molecular Genetics, Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA.,Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT 05405, USA
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8
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Banerjee AK, Blanco MR, Bruce EA, Honson DD, Chen LM, Chow A, Bhat P, Ollikainen N, Quinodoz SA, Loney C, Thai J, Miller ZD, Lin AE, Schmidt MM, Stewart DG, Goldfarb D, De Lorenzo G, Rihn SJ, Voorhees RM, Botten JW, Majumdar D, Guttman M. SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses. Cell 2020; 183:1325-1339.e21. [PMID: 33080218 PMCID: PMC7543886 DOI: 10.1016/j.cell.2020.10.004] [Citation(s) in RCA: 352] [Impact Index Per Article: 88.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/26/2020] [Accepted: 10/02/2020] [Indexed: 12/26/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recently identified coronavirus that causes the respiratory disease known as coronavirus disease 2019 (COVID-19). Despite the urgent need, we still do not fully understand the molecular basis of SARS-CoV-2 pathogenesis. Here, we comprehensively define the interactions between SARS-CoV-2 proteins and human RNAs. NSP16 binds to the mRNA recognition domains of the U1 and U2 splicing RNAs and acts to suppress global mRNA splicing upon SARS-CoV-2 infection. NSP1 binds to 18S ribosomal RNA in the mRNA entry channel of the ribosome and leads to global inhibition of mRNA translation upon infection. Finally, NSP8 and NSP9 bind to the 7SL RNA in the signal recognition particle and interfere with protein trafficking to the cell membrane upon infection. Disruption of each of these essential cellular functions acts to suppress the interferon response to viral infection. Our results uncover a multipronged strategy utilized by SARS-CoV-2 to antagonize essential cellular processes to suppress host defenses. NSP16 binds mRNA recognition domains of U1/U2 snRNAs and disrupts mRNA splicing NSP1 binds in the mRNA entry channel of the ribosome to disrupt protein translation NSP8 and NSP9 bind the signal recognition particle and disrupt protein trafficking These disruptions of protein production suppress the interferon response to infection
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Affiliation(s)
- Abhik K Banerjee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Mario R Blanco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Emily A Bruce
- Departments of Medicine, Division of Immunobiology and Microbiology, and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Drew D Honson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Linlin M Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Amy Chow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Prashant Bhat
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Noah Ollikainen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sofia A Quinodoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Colin Loney
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, UK
| | - Jasmine Thai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Zachary D Miller
- Department of Surgery and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Aaron E Lin
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Madaline M Schmidt
- Departments of Medicine, Division of Immunobiology and Microbiology, and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Douglas G Stewart
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, UK
| | - Daniel Goldfarb
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, UK
| | - Giuditta De Lorenzo
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, UK
| | - Suzannah J Rihn
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, UK
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jason W Botten
- Departments of Medicine, Division of Immunobiology and Microbiology, and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Devdoot Majumdar
- Department of Surgery and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA.
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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9
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Graham NR, Whitaker AN, Strother CA, Miles AK, Grier D, McElvany BD, Bruce EA, Poynter ME, Pierce KK, Kirkpatrick BD, Stapleton RD, An G, van den Broek‐Altenburg E, Botten JW, Crothers JW, Diehl SA. Kinetics and isotype assessment of antibodies targeting the spike protein receptor-binding domain of severe acute respiratory syndrome-coronavirus-2 in COVID-19 patients as a function of age, biological sex and disease severity. Clin Transl Immunology 2020; 9:e1189. [PMID: 33072323 PMCID: PMC7541824 DOI: 10.1002/cti2.1189] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/11/2020] [Accepted: 09/11/2020] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVES There is an incomplete understanding of the host humoral immune response to severe acute respiratory syndrome (SARS)-coronavirus (CoV)-2, which underlies COVID-19, during acute infection. Host factors such as age and sex as well as the kinetics and functionality of antibody responses are important factors to consider as vaccine development proceeds. The receptor-binding domain of the CoV spike (RBD-S) protein mediates host cell binding and infection and is a major target for vaccine design to elicit neutralising antibodies. METHODS We assessed serum anti-SARS-CoV-2 RBD-S IgG, IgM and IgA antibodies by a two-step ELISA and neutralising antibodies in a cross-sectional study of hospitalised COVID-19 patients of varying disease severities. Anti-RBD-S IgG levels were also determined in asymptomatic seropositives. RESULTS We found equivalent levels of anti-RBD-S antibodies in male and female patients and no age-related deficiencies even out to 93 years of age. The anti-RBD-S response was evident as little as 6 days after onset of symptoms and for at least 5 weeks after symptom onset. Anti-RBD-S IgG, IgM and IgA responses were simultaneously induced within 10 days after onset, with anti-RBD-S IgG sustained over a 5-week period. Anti-RBD-S antibodies strongly correlated with neutralising activity. Lastly, anti-RBD-S IgG responses were higher in symptomatic COVID-19 patients during acute infection compared with asymptomatic seropositive donors. CONCLUSION Our results suggest that anti-RBD-S IgG reflect functional immune responses to SARS-CoV-2, but do not completely explain age- and sex-related disparities in COVID-19 fatalities.
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Affiliation(s)
- Nancy R Graham
- Department of Microbiology and Molecular GeneticsLarner College of Medicine, University of VermontBurlingtonVTUSA
- Vaccine Testing CenterLarner College of Medicine, University of VermontBurlingtonVTUSA
| | - Annalis N Whitaker
- Department of Medicine‐ImmunobiologyLarner College of Medicine, University of VermontBurlingtonVTUSA
- Cellular, Molecular, and Biomedical Sciences Graduate ProgramUniversity of VermontBurlingtonVTUSA
- Vermont Center for Immunology and Infectious DiseaseLarner College of Medicine, University of VermontBurlingtonVTUSA
| | - Camilla A Strother
- Department of Microbiology and Molecular GeneticsLarner College of Medicine, University of VermontBurlingtonVTUSA
- Cellular, Molecular, and Biomedical Sciences Graduate ProgramUniversity of VermontBurlingtonVTUSA
| | - Ashley K Miles
- Department of Microbiology and Molecular GeneticsLarner College of Medicine, University of VermontBurlingtonVTUSA
- Vaccine Testing CenterLarner College of Medicine, University of VermontBurlingtonVTUSA
| | - Dore Grier
- Department of Pathology and Laboratory MedicineLarner College of Medicine, University of VermontBurlingtonVTUSA
| | - Benjamin D McElvany
- Department of Microbiology and Molecular GeneticsLarner College of Medicine, University of VermontBurlingtonVTUSA
- Vaccine Testing CenterLarner College of Medicine, University of VermontBurlingtonVTUSA
| | - Emily A Bruce
- Department of Medicine‐ImmunobiologyLarner College of Medicine, University of VermontBurlingtonVTUSA
- Vermont Center for Immunology and Infectious DiseaseLarner College of Medicine, University of VermontBurlingtonVTUSA
- Translational Global Infectious Disease Research CenterUniversity of VermontBurlingtonVTUSA
| | - Matthew E Poynter
- Cellular, Molecular, and Biomedical Sciences Graduate ProgramUniversity of VermontBurlingtonVTUSA
- Vermont Center for Immunology and Infectious DiseaseLarner College of Medicine, University of VermontBurlingtonVTUSA
- Translational Global Infectious Disease Research CenterUniversity of VermontBurlingtonVTUSA
- Vermont Lung CenterLarner College of Medicine, University of VermontBurlingtonVTUSA
- Department of Medicine‐Pulmonary and Critical CareLarner College of Medicine, University of VermontBurlingtonVTUSA
| | - Kristen K Pierce
- Department of Microbiology and Molecular GeneticsLarner College of Medicine, University of VermontBurlingtonVTUSA
- Vaccine Testing CenterLarner College of Medicine, University of VermontBurlingtonVTUSA
- Translational Global Infectious Disease Research CenterUniversity of VermontBurlingtonVTUSA
- Department of Medicine‐Infectious DiseaseLarner College of Medicine University of VermontBurlingtonVTUSA
| | - Beth D Kirkpatrick
- Department of Microbiology and Molecular GeneticsLarner College of Medicine, University of VermontBurlingtonVTUSA
- Vaccine Testing CenterLarner College of Medicine, University of VermontBurlingtonVTUSA
- Vermont Center for Immunology and Infectious DiseaseLarner College of Medicine, University of VermontBurlingtonVTUSA
- Translational Global Infectious Disease Research CenterUniversity of VermontBurlingtonVTUSA
- Department of Medicine‐Infectious DiseaseLarner College of Medicine University of VermontBurlingtonVTUSA
| | - Renee D Stapleton
- Vermont Lung CenterLarner College of Medicine, University of VermontBurlingtonVTUSA
- Department of Medicine‐Pulmonary and Critical CareLarner College of Medicine, University of VermontBurlingtonVTUSA
| | - Gary An
- Translational Global Infectious Disease Research CenterUniversity of VermontBurlingtonVTUSA
- Department of SurgeryLarner College of Medicine, University of VermontBurlingtonVTUSA
| | | | - Jason W Botten
- Department of Microbiology and Molecular GeneticsLarner College of Medicine, University of VermontBurlingtonVTUSA
- Vaccine Testing CenterLarner College of Medicine, University of VermontBurlingtonVTUSA
- Department of Medicine‐ImmunobiologyLarner College of Medicine, University of VermontBurlingtonVTUSA
- Cellular, Molecular, and Biomedical Sciences Graduate ProgramUniversity of VermontBurlingtonVTUSA
- Vermont Center for Immunology and Infectious DiseaseLarner College of Medicine, University of VermontBurlingtonVTUSA
- Translational Global Infectious Disease Research CenterUniversity of VermontBurlingtonVTUSA
| | - Jessica W Crothers
- Vermont Center for Immunology and Infectious DiseaseLarner College of Medicine, University of VermontBurlingtonVTUSA
- Translational Global Infectious Disease Research CenterUniversity of VermontBurlingtonVTUSA
- Department of Medicine‐Infectious DiseaseLarner College of Medicine University of VermontBurlingtonVTUSA
| | - Sean A Diehl
- Department of Microbiology and Molecular GeneticsLarner College of Medicine, University of VermontBurlingtonVTUSA
- Vaccine Testing CenterLarner College of Medicine, University of VermontBurlingtonVTUSA
- Cellular, Molecular, and Biomedical Sciences Graduate ProgramUniversity of VermontBurlingtonVTUSA
- Vermont Center for Immunology and Infectious DiseaseLarner College of Medicine, University of VermontBurlingtonVTUSA
- Translational Global Infectious Disease Research CenterUniversity of VermontBurlingtonVTUSA
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10
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Bruce EA, Huang ML, Perchetti GA, Tighe S, Laaguiby P, Hoffman JJ, Gerrard DL, Nalla AK, Wei Y, Greninger AL, Diehl SA, Shirley DJ, Leonard DGB, Huston CD, Kirkpatrick BD, Dragon JA, Crothers JW, Jerome KR, Botten JW. Direct RT-qPCR detection of SARS-CoV-2 RNA from patient nasopharyngeal swabs without an RNA extraction step. PLoS Biol 2020; 18:e3000896. [PMID: 33006983 PMCID: PMC7556528 DOI: 10.1371/journal.pbio.3000896] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 10/14/2020] [Accepted: 09/10/2020] [Indexed: 11/24/2022] Open
Abstract
The ongoing COVID-19 pandemic has created an unprecedented need for rapid diagnostic testing. The World Health Organization (WHO) recommends a standard assay that includes an RNA extraction step from a nasopharyngeal (NP) swab followed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to detect the purified SARS-CoV-2 RNA. The current global shortage of RNA extraction kits has caused a severe bottleneck to COVID-19 testing. The goal of this study was to determine whether SARS-CoV-2 RNA could be detected from NP samples via a direct RT-qPCR assay that omits the RNA extraction step altogether. The direct RT-qPCR approach correctly identified 92% of a reference set of blinded NP samples (n = 155) demonstrated to be positive for SARS-CoV-2 RNA by traditional clinical diagnostic RT-qPCR that included an RNA extraction. Importantly, the direct method had sufficient sensitivity to reliably detect those patients with viral loads that correlate with the presence of infectious virus. Thus, this strategy has the potential to ease supply choke points to substantially expand COVID-19 testing and screening capacity and should be applicable throughout the world.
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Affiliation(s)
- Emily A. Bruce
- Division of Immunobiology, Department of Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Meei-Li Huang
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Garrett A. Perchetti
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Scott Tighe
- Vermont Integrative Genomics Resource, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Pheobe Laaguiby
- Vermont Integrative Genomics Resource, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Jessica J. Hoffman
- Vermont Integrative Genomics Resource, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Diana L. Gerrard
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, Vermont, United States of America
| | - Arun K. Nalla
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Yulun Wei
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Alexander L. Greninger
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Sean A. Diehl
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Vaccine Testing Center, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - David J. Shirley
- Data Science Division, IXIS, Burlington, Vermont, United States of America
| | - Debra G. B. Leonard
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- University of Vermont Health Network, Burlington, Vermont, United States of America
| | - Christopher D. Huston
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Division of Infectious Disease, Department of Medicine, University of Vermont Medical Center, Burlington, Vermont, United States of America
| | - Beth D. Kirkpatrick
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Vaccine Testing Center, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Division of Infectious Disease, Department of Medicine, University of Vermont Medical Center, Burlington, Vermont, United States of America
| | - Julie A. Dragon
- Vermont Integrative Genomics Resource, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Jessica W. Crothers
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- University of Vermont Health Network, Burlington, Vermont, United States of America
| | - Keith R. Jerome
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jason W. Botten
- Division of Immunobiology, Department of Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Vaccine Testing Center, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
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11
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Vial C, Whitaker A, Wilhelm J, Ovalle J, Perez R, Valdivieso F, Ferres M, Martinez-Valdebenito C, Eisenhauer P, Mertz GJ, Hooper JW, Botten JW, Vial PA. Comparison of VSV Pseudovirus and Focus Reduction Neutralization Assays for Measurement of Anti- Andes orthohantavirus Neutralizing Antibodies in Patient Samples. Front Cell Infect Microbiol 2020; 10:444. [PMID: 33042854 PMCID: PMC7527604 DOI: 10.3389/fcimb.2020.00444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/20/2020] [Indexed: 12/24/2022] Open
Abstract
Andes orthohantavirus (ANDV) is the etiologic agent of hantavirus cardiopulmonary syndrome (HCPS), which has a case fatality rate around 35%, with no effective treatment or vaccine available. ANDV neutralizing antibody (NAb) measurements are important for the evaluation of the immune response following infection, vaccination, or passive administration of investigational monoclonal or polyclonal antibodies. The standard assay for NAb measurement is a focus reduction neutralization test (FRNT) featuring live ANDV and must be completed under biosafety level (BSL)-3 conditions. In this study, we compared neutralization assays featuring infectious ANDV or vesicular stomatitis virus (VSV) pseudovirions decorated with ANDV glycoproteins for their ability to measure anti-ANDV NAbs from patient samples. Our studies demonstrate that VSV pseudovirions effectively measure NAb from clinical samples and have greater sensitivity compared to FRNT with live ANDV. Importantly, the pseudovirus assay requires less labor and sample materials and can be conducted at BSL-2.
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Affiliation(s)
- Cecilia Vial
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Programa Hantavirus, Instituto de Ciencias e Innovación en Medicina, Santiago, Chile
| | - Annalis Whitaker
- Division of Immunobiology, Department of Medicine, University of Vermont, Burlington, VT, United States
- Cellular, Molecular and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT, United States
| | - Jan Wilhelm
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Programa Hantavirus, Instituto de Ciencias e Innovación en Medicina, Santiago, Chile
- Clínica Alemana de Santiago, Santiago, Chile
| | - Jimena Ovalle
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Programa Hantavirus, Instituto de Ciencias e Innovación en Medicina, Santiago, Chile
| | - Ruth Perez
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Programa Hantavirus, Instituto de Ciencias e Innovación en Medicina, Santiago, Chile
| | | | - Marcela Ferres
- Laboratorio de Infectología y Virología Molecular, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Facultad de Medicina Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Constanza Martinez-Valdebenito
- Laboratorio de Infectología y Virología Molecular, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Facultad de Medicina Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Philip Eisenhauer
- Division of Immunobiology, Department of Medicine, University of Vermont, Burlington, VT, United States
| | - Gregory J. Mertz
- Division of Infectious Diseases, Department of Internal Medicine University of New Mexico, Albuquerque, NM, United States
| | - Jay W. Hooper
- Molecular Virology Branch, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Jason W. Botten
- Division of Immunobiology, Department of Medicine, University of Vermont, Burlington, VT, United States
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, United States
| | - Pablo A. Vial
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Programa Hantavirus, Instituto de Ciencias e Innovación en Medicina, Santiago, Chile
- Clínica Alemana de Santiago, Santiago, Chile
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12
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Drayman N, Jones KA, Azizi SA, Froggatt HM, Tan K, Maltseva NI, Chen S, Nicolaescu V, Dvorkin S, Furlong K, Kathayat RS, Firpo MR, Mastrodomenico V, Bruce EA, Schmidt MM, Jedrzejczak R, Muñoz-Alía MÁ, Schuster B, Nair V, Botten JW, Brooke CB, Baker SC, Mounce BC, Heaton NS, Dickinson BC, Jaochimiak A, Randall G, Tay S. Drug repurposing screen identifies masitinib as a 3CLpro inhibitor that blocks replication of SARS-CoV-2 in vitro. bioRxiv 2020. [PMID: 32908976 DOI: 10.1101/2020.08.31.274639] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
There is an urgent need for anti-viral agents that treat SARS-CoV-2 infection. The shortest path to clinical use is repurposing of drugs that have an established safety profile in humans. Here, we first screened a library of 1,900 clinically safe drugs for inhibiting replication of OC43, a human beta-coronavirus that causes the common-cold and is a relative of SARS-CoV-2, and identified 108 effective drugs. We further evaluated the top 26 hits and determined their ability to inhibit SARS-CoV-2, as well as other pathogenic RNA viruses. 20 of the 26 drugs significantly inhibited SARS-CoV-2 replication in human lung cells (A549 epithelial cell line), with EC50 values ranging from 0.1 to 8 micromolar. We investigated the mechanism of action for these and found that masitinib, a drug originally developed as a tyrosine-kinase inhibitor for cancer treatment, strongly inhibited the activity of the SARS-CoV-2 main protease 3CLpro. X-ray crystallography revealed that masitinib directly binds to the active site of 3CLpro, thereby blocking its enzymatic activity. Mastinib also inhibited the related viral protease of picornaviruses and blocked picornaviruses replication. Thus, our results show that masitinib has broad anti-viral activity against two distinct beta-coronaviruses and multiple picornaviruses that cause human disease and is a strong candidate for clinical trials to treat SARS-CoV-2 infection.
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13
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Graham NR, Whitaker AN, Strother CA, Miles AK, Grier D, McElvany BD, Bruce EA, Poynter ME, Pierce KK, Kirkpatrick BD, Stapleton RD, An G, Botten JW, Crothers JW, Diehl SA. Kinetics and Isotype Assessment of Antibodies Targeting the Spike Protein Receptor Binding Domain of SARS-CoV-2 In COVID-19 Patients as a function of Age and Biological Sex. medRxiv 2020:2020.07.15.20154443. [PMID: 32743592 PMCID: PMC7386516 DOI: 10.1101/2020.07.15.20154443] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
SARS-CoV-2 is the newly emerged virus responsible for the global COVID-19 pandemic. There is an incomplete understanding of the host humoral immune response to SARS-CoV-2 during acute infection. Host factors such as age and sex as well the kinetics and functionality of antibody responses are important factors to consider as vaccine development proceeds. The receptor-binding domain of the CoV spike (RBD-S) protein is important in host cell recognition and infection and antibodies targeting this domain are often neutralizing. In a cross-sectional study of anti-RBD-S antibodies in COVID-19 patients we found equivalent levels in male and female patients and no age-related deficiencies even out to 93 years of age. The anti-RBD-S response was evident as little as 6 days after onset of symptoms and for at least 5 weeks after symptom onset. Anti-RBD-S IgG, IgM, and IgA responses were simultaneously induced within 10 days after onset, but isotype-specific kinetics differed such that anti-RBD-S IgG was most sustained over a 5-week period. The kinetics and magnitude of neutralizing antibody formation strongly correlated with that seen for anti-RBD-S antibodies. Our results suggest age- and sex- related disparities in COVID-19 fatalities are not explained by anti-RBD-S responses. The multi-isotype anti-RBD-S response induced by live virus infection could serve as a potential marker by which to monitor vaccine-induced responses.
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Abstract
Viral defective interfering particles (DIPs) were intensely studied several decades ago but research waned leaving open many critical questions. New technologies and other advances led to a resurgence in DIP studies for negative-strand RNA viruses. While DIPs have long been recognized, their exact contribution to the outcome of acute or persistent viral infections has remained elusive. Recent studies have identified defective viral genomes (DVGs) in human infections, including respiratory syncytial virus and influenza, and growing evidence indicates that DVGs influence disease severity and may contribute to viral persistence. Further, several studies have advanced our understanding of key viral and host factors that regulate DIP formation and activity. Here we review these discoveries and highlight key questions moving forward.
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Affiliation(s)
- Christopher M Ziegler
- Department of Medicine, Division of Immunobiology, University of Vermont, Burlington, VT 05405, USA
| | - Jason W Botten
- Department of Medicine, Division of Immunobiology, University of Vermont, Burlington, VT 05405, USA; Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; Vaccine Testing Center, University of Vermont, Burlington, VT 05405, USA.
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15
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Pettit SD, Jerome KR, Rouquié D, Mari B, Barbry P, Kanda Y, Matsumoto M, Hester S, Wehmas L, Botten JW, Bruce EA. 'All In': a pragmatic framework for COVID-19 testing and action on a global scale. EMBO Mol Med 2020; 12:e12634. [PMID: 32375201 PMCID: PMC7267598 DOI: 10.15252/emmm.202012634] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Current demand for SARS-CoV-2 testing is straining material resource and labor capacity around the globe. As a result, the public health and clinical community are hindered in their ability to monitor and contain the spread of COVID-19. Despite broad consensus that more testing is needed, pragmatic guidance toward realizing this objective has been limited. This paper addresses this limitation by proposing a novel and geographically agnostic framework (the 4Ps framework) to guide multidisciplinary, scalable, resource-efficient, and achievable efforts toward enhanced testing capacity. The 4Ps (Prioritize, Propagate, Partition, and Provide) are described in terms of specific opportunities to enhance the volume, diversity, characterization, and implementation of SARS-CoV-2 testing to benefit public health. Coordinated deployment of the strategic and tactical recommendations described in this framework has the potential to rapidly expand available testing capacity, improve public health decision-making in response to the COVID-19 pandemic, and/or to be applied in future emergent disease outbreaks.
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Affiliation(s)
- Syril D Pettit
- Health and Environmental Sciences InstituteWashingtonDCUSA
| | - Keith R Jerome
- Virology DivisionDepartment of Laboratory MedicineUniversity of WashingtonSeattleWAUSA
| | | | - Bernard Mari
- Institut de Pharmacologie Moléculaire et Cellulaire (IPMC)CNRSUniversité Côte d'AzurValbonneFrance
| | - Pascal Barbry
- Institut de Pharmacologie Moléculaire et Cellulaire (IPMC)CNRSUniversité Côte d'AzurValbonneFrance
| | | | | | - Susan Hester
- Office of Research and DevelopmentEnvironmental Protection AgencyResearch Triangle ParkNCUSA
| | - Leah Wehmas
- Office of Research and DevelopmentEnvironmental Protection AgencyResearch Triangle ParkNCUSA
| | - Jason W Botten
- Division of ImmunobiologyDepartment of MedicineLarner College of MedicineUniversity of VermontBurlingtonVTUSA
| | - Emily A Bruce
- Division of ImmunobiologyDepartment of MedicineLarner College of MedicineUniversity of VermontBurlingtonVTUSA
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16
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Bruce EA, Huang ML, Perchetti GA, Tighe S, Laaguiby P, Hoffman JJ, Gerrard DL, Nalla AK, Wei Y, Greninger AL, Diehl SA, Shirley DJ, Leonard DGB, Huston CD, Kirkpatrick BD, Dragon JA, Crothers JW, Jerome KR, Botten JW. DIRECT RT-qPCR DETECTION OF SARS-CoV-2 RNA FROM PATIENT NASOPHARYNGEAL SWABS WITHOUT AN RNA EXTRACTION STEP. bioRxiv 2020:2020.03.20.001008. [PMID: 32511328 PMCID: PMC7239058 DOI: 10.1101/2020.03.20.001008] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The ongoing COVID-19 pandemic has caused an unprecedented need for rapid diagnostic testing. The Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) recommend a standard assay that includes an RNA extraction step from a nasopharyngeal (NP) swab followed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to detect the purified SARS-CoV-2 RNA. The current global shortage of RNA extraction kits has caused a severe bottleneck to COVID-19 testing. We hypothesized that SARS-CoV-2 RNA could be detected from NP samples via a direct RT-qPCR assay that omits the RNA extraction step altogether, and tested this hypothesis on a series of blinded clinical samples. The direct RT-qPCR approach correctly identified 92% of NP samples (n = 155) demonstrated to be positive for SARS-CoV-2 RNA by traditional clinical diagnostic RT-qPCR that included an RNA extraction. Thus, direct RT-qPCR could be a front-line approach to identify the substantial majority of COVID-19 patients, reserving a repeat test with RNA extraction for those individuals with high suspicion of infection but an initial negative result. This strategy would drastically ease supply chokepoints of COVID-19 testing and should be applicable throughout the world.
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Affiliation(s)
- Emily A. Bruce
- Department of Medicine, Division of Immunobiology, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Meei-Li Huang
- Virology Division, Department of Laboratory Medicine, University of Washington, Seattle WA 98195, USA
| | - Garrett A. Perchetti
- Virology Division, Department of Laboratory Medicine, University of Washington, Seattle WA 98195, USA
| | - Scott Tighe
- Vermont Integrative Genomics Resource, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Pheobe Laaguiby
- Vermont Integrative Genomics Resource, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Jessica J. Hoffman
- Vermont Integrative Genomics Resource, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Diana L. Gerrard
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington VT, 05401, USA
| | - Arun K. Nalla
- Virology Division, Department of Laboratory Medicine, University of Washington, Seattle WA 98195, USA
| | - Yulun Wei
- Virology Division, Department of Laboratory Medicine, University of Washington, Seattle WA 98195, USA
| | - Alexander L. Greninger
- Virology Division, Department of Laboratory Medicine, University of Washington, Seattle WA 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA 98109, USA
| | - Sean A. Diehl
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
- Vaccine Testing Center, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405 USA
| | | | - Debra G. B. Leonard
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont and the University of Vermont Health Network, Burlington VT, 05405, USA
| | - Christopher D. Huston
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
- Department of Medicine, Division of Infectious Disease, University of Vermont Medical Center, Burlington VT, 05401, USA
| | - Beth D. Kirkpatrick
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
- Vaccine Testing Center, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405 USA
- Department of Medicine, Division of Infectious Disease, University of Vermont Medical Center, Burlington VT, 05401, USA
| | - Julie A. Dragon
- Vermont Integrative Genomics Resource, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Jessica W. Crothers
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont and the University of Vermont Health Network, Burlington VT, 05405, USA
| | - Keith R. Jerome
- Virology Division, Department of Laboratory Medicine, University of Washington, Seattle WA 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA 98109, USA
| | - Jason W. Botten
- Department of Medicine, Division of Immunobiology, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
- Vaccine Testing Center, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405 USA
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17
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Graham N, Eisenhauer P, Diehl SA, Pierce KK, Whitehead SS, Durbin AP, Kirkpatrick BD, Sette A, Weiskopf D, Boyson JE, Botten JW. Rapid Induction and Maintenance of Virus-Specific CD8 + T EMRA and CD4 + T EM Cells Following Protective Vaccination Against Dengue Virus Challenge in Humans. Front Immunol 2020; 11:479. [PMID: 32265929 PMCID: PMC7105617 DOI: 10.3389/fimmu.2020.00479] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 03/02/2020] [Indexed: 11/17/2022] Open
Abstract
Dengue virus (DENV) is a mosquito-borne flavivirus that causes serious human disease. The current lack of an effective vaccine to simultaneously protect against the four serotypes of DENV in seronegative individuals is a major unmet medical need. Further, the immunological basis for protective immunity in the setting of DENV infection or vaccination is not fully understood. Our team has developed a live attenuated tetravalent dengue virus vaccine that provides complete protection in a human model of dengue virus challenge. The goal of this study was to define, in the context of protective human vaccination, the quality of vaccine-induced DENV-specific CD8+ and CD4+ T cells and the temporal dynamics associated with their formation and maintenance. Multifunctional, DENV-specific CD8+ and CD4+ T cells developed 8-14 days after vaccination and were maintained for at least 6 months. Virus-specific CD8 T+ cells were a mixture of effector memory T cells (TEM) and effector memory T cells re-expressing CD45RA (TEMRA), with TEM cells predominating until day 21 post-vaccination and TEMRA cells thereafter. The majority of virus-specific CD4+ T cells were TEM with a small fraction being TEMRA. The frequency of virus-specific CD8+ and CD4+ T cells were further skewed to the TEMRA phenotype following either a second dose of the tetravalent vaccine or challenge with a single serotype of DENV. Collectively, our study has defined the phenotypic profile of antiviral CD8+ and CD4+ T cells associated with protective immunity to DENV infection and the kinetics of their formation and maintenance.
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Affiliation(s)
- Nancy Graham
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, United States
- Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT, United States
| | - Phil Eisenhauer
- Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT, United States
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, United States
| | - Sean A. Diehl
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, United States
- Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT, United States
| | - Kristen K. Pierce
- Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT, United States
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, United States
| | - Stephen S. Whitehead
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Anna P. Durbin
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Beth D. Kirkpatrick
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, United States
- Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT, United States
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
- Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Jonathan E. Boyson
- Department of Surgery, Larner College of Medicine, University of Vermont, Burlington, VT, United States
| | - Jason W. Botten
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, United States
- Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT, United States
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, United States
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18
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Ziegler CM, Bruce EA, Kelly JA, King BR, Botten JW. The use of novel epitope-tagged arenaviruses reveals that Rab5c-positive endosomal membranes are targeted by the LCMV matrix protein. J Gen Virol 2019; 99:187-193. [PMID: 29393022 DOI: 10.1099/jgv.0.001004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We report the development of recombinant New World (Junín; JUNV) and Old World (lymphocytic choriomeningitis virus; LCMV) mammarenaviruses that encode an HA-tagged matrix protein (Z). These viruses permit the robust affinity purification of Z from infected cells or virions, as well as the detection of Z by immunofluorescent microscopy. Importantly, the HA-tagged viruses grow with wild-type kinetics in a multi-cycle growth assay. Using these viruses, we report a novel description of JUNV Z localization in infected cells, as well as the first description of colocalization between LCMV Z and the GTPase Rab5c. This latter result, when combined with our previous findings that LCMV genome and glycoprotein also colocalize with Rab5c, suggest that LCMV may target Rab5c-positive membranes for preassembly of virus particles prior to budding. The recombinant viruses reported here will provide the field with new tools to better study Z protein functionality and identify key Z protein interactions with host machinery.
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Affiliation(s)
- Christopher M Ziegler
- Department of Medicine, Division of Immunobiology, University of Vermont, Burlington, VT 05405, USA.,Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT 05405, USA
| | - Emily A Bruce
- Department of Medicine, Division of Immunobiology, University of Vermont, Burlington, VT 05405, USA
| | - Jamie A Kelly
- Department of Medicine, Division of Immunobiology, University of Vermont, Burlington, VT 05405, USA
| | - Benjamin R King
- Department of Medicine, Division of Immunobiology, University of Vermont, Burlington, VT 05405, USA.,Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT 05405, USA
| | - Jason W Botten
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA.,Department of Medicine, Division of Immunobiology, University of Vermont, Burlington, VT 05405, USA
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19
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Burgess EJ, Hoyt LR, Randall MJ, Mank MM, Bivona JJ, Eisenhauer PL, Botten JW, Ballif BA, Lam YW, Wargo MJ, Boyson JE, Ather JL, Poynter ME. Bacterial Lipoproteins Constitute the TLR2-Stimulating Activity of Serum Amyloid A. J Immunol 2018; 201:2377-2384. [PMID: 30158125 PMCID: PMC6179936 DOI: 10.4049/jimmunol.1800503] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 08/04/2018] [Indexed: 12/21/2022]
Abstract
Studies comparing endogenous and recombinant serum amyloid A (SAA) have generated conflicting data on the proinflammatory function of these proteins. In exploring this discrepancy, we found that in contrast to commercially sourced recombinant human SAA1 (hSAA1) proteins produced in Escherichia coli, hSAA1 produced from eukaryotic cells did not promote proinflammatory cytokine production from human or mouse cells, induce Th17 differentiation, or stimulate TLR2. Proteomic analysis of E. coli-derived hSAA1 revealed the presence of numerous bacterial proteins, with several being reported or probable lipoproteins. Treatment of hSAA1 with lipoprotein lipase or addition of a lipopeptide to eukaryotic cell-derived hSAA1 inhibited or induced the production of TNF-α from macrophages, respectively. Our results suggest that a function of SAA is in the binding of TLR2-stimulating bacterial proteins, including lipoproteins, and demand that future studies of SAA employ a recombinant protein derived from eukaryotic cells.
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Affiliation(s)
- Edward J Burgess
- Vermont Lung Center, University of Vermont, Burlington, VT 05405
- Cellular, Molecular, and Biomedical Sciences Program, University of Vermont, Burlington, VT 05405
- Division of Pulmonary Disease and Critical Care, Department of Medicine, University of Vermont, Burlington, VT 05405
| | - Laura R Hoyt
- Vermont Lung Center, University of Vermont, Burlington, VT 05405
- Division of Pulmonary Disease and Critical Care, Department of Medicine, University of Vermont, Burlington, VT 05405
| | - Matthew J Randall
- Vermont Lung Center, University of Vermont, Burlington, VT 05405
- Division of Pulmonary Disease and Critical Care, Department of Medicine, University of Vermont, Burlington, VT 05405
| | - Madeleine M Mank
- Vermont Lung Center, University of Vermont, Burlington, VT 05405
- Division of Pulmonary Disease and Critical Care, Department of Medicine, University of Vermont, Burlington, VT 05405
| | - Joseph J Bivona
- Vermont Lung Center, University of Vermont, Burlington, VT 05405
- Cellular, Molecular, and Biomedical Sciences Program, University of Vermont, Burlington, VT 05405
- Division of Pulmonary Disease and Critical Care, Department of Medicine, University of Vermont, Burlington, VT 05405
| | - Philip L Eisenhauer
- Immunobiology Division, Department of Medicine, University of Vermont, Burlington, VT 05405
| | - Jason W Botten
- Vermont Lung Center, University of Vermont, Burlington, VT 05405
- Cellular, Molecular, and Biomedical Sciences Program, University of Vermont, Burlington, VT 05405
- Immunobiology Division, Department of Medicine, University of Vermont, Burlington, VT 05405
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405
| | - Bryan A Ballif
- Department of Biology, University of Vermont, Burlington, VT 05405; and
| | - Ying-Wai Lam
- Department of Biology, University of Vermont, Burlington, VT 05405; and
| | - Matthew J Wargo
- Vermont Lung Center, University of Vermont, Burlington, VT 05405
- Cellular, Molecular, and Biomedical Sciences Program, University of Vermont, Burlington, VT 05405
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405
| | - Jonathan E Boyson
- Vermont Lung Center, University of Vermont, Burlington, VT 05405
- Cellular, Molecular, and Biomedical Sciences Program, University of Vermont, Burlington, VT 05405
- Department of Surgery, University of Vermont, Burlington, VT 05405
| | - Jennifer L Ather
- Vermont Lung Center, University of Vermont, Burlington, VT 05405
- Division of Pulmonary Disease and Critical Care, Department of Medicine, University of Vermont, Burlington, VT 05405
| | - Matthew E Poynter
- Vermont Lung Center, University of Vermont, Burlington, VT 05405;
- Cellular, Molecular, and Biomedical Sciences Program, University of Vermont, Burlington, VT 05405
- Division of Pulmonary Disease and Critical Care, Department of Medicine, University of Vermont, Burlington, VT 05405
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20
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Abstract
Lymphocytic choriomeningitis virus (LCMV) is one of the most studied infectious disease models in mice. Human infection with LCMV can result in severe disease, ranging from aseptic meningitis in immunocompetent individuals, hydrocephalus, chorioretinitis or microcephaly in fetal infection, or to a highly lethal outcome in immunosuppressed individuals. This review examines recent advances in our understanding of the adaptive immune response to LCMV and how the cell-mediated and humoral immune responses contribute to protective immunity. New insights into the antigenicity of the LCMV proteome and the complexity of the cell-mediated immune response are addressed. We also discuss state-of-the-art approaches for T-cell epitope discovery in murine and human backgrounds and their recent application to LCMV. New findings regarding CD4+ T-cell dysregulation during chronic LCMV infection, and potential avenues for the treatment of chronic viral infection through modulation of the programmed cell death-1 receptor and/or IL-10 signaling pathways, are also evaluated.
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Affiliation(s)
- Jason W Botten
- The Scripps Research Institute, Molecular & Integrative Neurosciences Department, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Maya F Kotturi
- La Jolla Institute for Allergy & Immunology, Division of Vaccine Discovery, 9420 Athena Circle, La Jolla, CA 92037, USA
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21
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Aho EL, Botten JW, Hall RJ, Larson MK, Ness JK. Characterization of a class II pilin expression locus from Neisseria meningitidis: evidence for increased diversity among pilin genes in pathogenic Neisseria species. Infect Immun 1997; 65:2613-20. [PMID: 9199428 PMCID: PMC175370 DOI: 10.1128/iai.65.7.2613-2620.1997] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Strains of Neisseria meningitidis elaborate one of two classes of pili. Meningococcal class I pili have many features in common with pili produced by N. gonorrhoeae, including the ability to bind monoclonal antibody SM1 and a common gene and protein structure consisting of conserved, semivariable, and hypervariable regions. Class II pili are SM1 nonreactive and display smaller subunit molecular weights than do gonococcal or meningococcal class I pili. In this study, we have determined the N-terminal amino acid sequence for class II pilin and isolated the expression locus encoding class II pilin from N. meningitidis FAM18. Meningococcal class II pilin displays features typical of type IV pili and shares extensive amino acid identity with the N-terminal conserved regions of other neisserial pilin proteins. However, the deduced class II pilin sequence displays several unique features compared with previously reported meningococcal class I and gonococcal pilin sequences. Class II pilin lacks several conserved peptide regions found within the semivariable and hypervariable regions of other neisserial pilins and displays a large deletion in a hypervariable region of the protein believed to be exposed on the pilus face in gonococcal pili. DNA sequence comparisons within all three regions of the coding sequence also suggest that the meningococcal class II pilin gene is the most dissimilar of the three types of neisserial pilE loci. Additionally, the class II locus fails to display flanking-sequence homology to class I and gonococcal genes and lacks a downstream Sma/Cla repeat sequence, a feature present in all other neisserial pilin genes examined to date. These data indicate meningococcal class II pili represent a structurally distinct class of pili and suggest that relationships among pilin genes in pathogenic Neisseria do not necessarily follow species boundaries.
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Affiliation(s)
- E L Aho
- Department of Biology, Concordia College, Moorhead, Minnesota 56562, USA.
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