101
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Dong T, Wang M, Liu J, Ma P, Pang S, Liu W, Liu A. Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives. Chem Sci 2023; 14:6149-6206. [PMID: 37325147 PMCID: PMC10266450 DOI: 10.1039/d2sc06665c] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/03/2023] [Indexed: 06/17/2023] Open
Abstract
The disastrous spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has induced severe public healthcare issues and weakened the global economy significantly. Although SARS-CoV-2 infection is not as fatal as the initial outbreak, many infected victims suffer from long COVID. Therefore, rapid and large-scale testing is critical in managing patients and alleviating its transmission. Herein, we review the recent advances in techniques to detect SARS-CoV-2. The sensing principles are detailed together with their application domains and analytical performances. In addition, the advantages and limits of each method are discussed and analyzed. Besides molecular diagnostics and antigen and antibody tests, we also review neutralizing antibodies and emerging SARS-CoV-2 variants. Further, the characteristics of the mutational locations in the different variants with epidemiological features are summarized. Finally, the challenges and possible strategies are prospected to develop new assays to meet different diagnostic needs. Thus, this comprehensive and systematic review of SARS-CoV-2 detection technologies may provide insightful guidance and direction for developing tools for the diagnosis and analysis of SARS-CoV-2 to support public healthcare and effective long-term pandemic management and control.
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Affiliation(s)
- Tao Dong
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
- School of Pharmacy, Medical College, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Mingyang Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Junchong Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Pengxin Ma
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Shuang Pang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Wanjian Liu
- Qingdao Hightop Biotech Co., Ltd 369 Hedong Road, Hi-tech Industrial Development Zone Qingdao 266112 China
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
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102
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Collett S, Earnest L, Carrera Montoya J, Edeling MA, Yap A, Wong CY, Christiansen D, Roberts J, Mumford J, Lecouturier V, Pavot V, Marco S, Loi JK, Simmons C, Gulab SA, Mackenzie JM, Elbourne A, Ramsland PA, Cameron G, Hans D, Godfrey DI, Torresi J. Development of virus-like particles with inbuilt immunostimulatory properties as vaccine candidates. Front Microbiol 2023; 14:1065609. [PMID: 37350788 PMCID: PMC10282183 DOI: 10.3389/fmicb.2023.1065609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 05/17/2023] [Indexed: 06/24/2023] Open
Abstract
The development of virus-like particle (VLP) based vaccines for human papillomavirus, hepatitis B and hepatitis E viruses represented a breakthrough in vaccine development. However, for dengue and COVID-19, technical complications, such as an incomplete understanding of the requirements for protective immunity, but also limitations in processes to manufacture VLP vaccines for enveloped viruses to large scale, have hampered VLP vaccine development. Selecting the right adjuvant is also an important consideration to ensure that a VLP vaccine induces protective antibody and T cell responses. For diseases like COVID-19 and dengue fever caused by RNA viruses that exist as families of viral variants with the potential to escape vaccine-induced immunity, the development of more efficacious vaccines is also necessary. Here, we describe the development and characterisation of novel VLP vaccine candidates using SARS-CoV-2 and dengue virus (DENV), containing the major viral structural proteins, as protypes for a novel approach to produce VLP vaccines. The VLPs were characterised by Western immunoblot, enzyme immunoassay, electron and atomic force microscopy, and in vitro and in vivo immunogenicity studies. Microscopy techniques showed proteins self-assemble to form VLPs authentic to native viruses. The inclusion of the glycolipid adjuvant, α-galactosylceramide (α-GalCer) in the vaccine formulation led to high levels of natural killer T (NKT) cell stimulation in vitro, and strong antibody and memory CD8+ T cell responses in vivo, demonstrated with SARS-CoV-2, hepatitis C virus (HCV) and DEN VLPs. This study shows our unique vaccine formulation presents a promising, and much needed, new vaccine platform in the fight against infections caused by enveloped RNA viruses.
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Affiliation(s)
- Simon Collett
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC, Australia
| | - Linda Earnest
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Julio Carrera Montoya
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Melissa A. Edeling
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Ashley Yap
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Chinn Yi Wong
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Dale Christiansen
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Jason Roberts
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Infectious Diseases, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jamie Mumford
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | | | | | - Joon Keit Loi
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Cameron Simmons
- Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia
| | - Shivali A. Gulab
- Avalia Immunotherapies Limited, Wellington, New Zealand
- Vaccine Alliance Aotearoa New Zealand, Wellington, New Zealand
| | - Jason M. Mackenzie
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Aaron Elbourne
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC, Australia
| | - Paul A. Ramsland
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC, Australia
- Department of Surgery Austin Health, University of Melbourne, Heidelberg, VIC, Australia
- Department of Immunology, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Garth Cameron
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Dhiraj Hans
- Research, Innovation and Commercialisation, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Dale I. Godfrey
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Joseph Torresi
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
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103
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Bloom JD, Neher RA. Fitness effects of mutations to SARS-CoV-2 proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526314. [PMID: 36778462 PMCID: PMC9915511 DOI: 10.1101/2023.01.30.526314] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Knowledge of the fitness effects of mutations to SARS-CoV-2 can inform assessment of new variants, design of therapeutics resistant to escape, and understanding of the functions of viral proteins. However, experimentally measuring effects of mutations is challenging: we lack tractable lab assays for many SARS-CoV-2 proteins, and comprehensive deep mutational scanning has been applied to only two SARS-CoV-2 proteins. Here we develop an approach that leverages millions of publicly available SARS-CoV-2 sequences to estimate effects of mutations. We first calculate how many independent occurrences of each mutation are expected to be observed along the SARS-CoV-2 phylogeny in the absence of selection. We then compare these expected observations to the actual observations to estimate the effect of each mutation. These estimates correlate well with deep mutational scanning measurements. For most genes, synonymous mutations are nearly neutral, stop-codon mutations are deleterious, and amino-acid mutations have a range of effects. However, some viral accessory proteins are under little to no selection. We provide interactive visualizations of effects of mutations to all SARS-CoV-2 proteins (https://jbloomlab.github.io/SARS2-mut-fitness/). The framework we describe is applicable to any virus for which the number of available sequences is sufficiently large that many independent occurrences of each neutral mutation are observed.
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Affiliation(s)
- Jesse D. Bloom
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Center
- Department of Genome Sciences, University of Washington
- Howard Hughes Medical Institute
| | - Richard A. Neher
- Biozentrum, University of Basel
- Swiss Institute of Bioinformatics
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104
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Kuzmina A, Korovin D, Cohen Lass I, Atari N, Ottolenghi A, Hu P, Mandelboim M, Rosental B, Rosenberg E, Diaz-Griffero F, Taube R. Changes within the P681 residue of spike dictate cell fusion and syncytia formation of Delta and Omicron variants of SARS-CoV-2 with no effects on neutralization or infectivity. Heliyon 2023; 9:e16750. [PMID: 37292300 PMCID: PMC10238279 DOI: 10.1016/j.heliyon.2023.e16750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 04/13/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023] Open
Abstract
The rapid spread and dominance of the Omicron SARS-CoV-2 lineages have posed severe health challenges worldwide. While extensive research on the role of the Receptor Binding Domain (RBD) in promoting viral infectivity and vaccine sensitivity has been well documented, the functional significance of the 681PRRAR/SV687 polybasic motif of the viral spike is less clear. In this work, we monitored the infectivity levels and neutralization potential of the wild-type human coronavirus 2019 (hCoV-19), Delta, and Omicron SARS-CoV-2 pseudoviruses against sera samples drawn four months post administration of a third dose of the BNT162b2 mRNA vaccine. Our findings show that in comparison to hCoV-19 and Delta SARS-CoV-2, Omicron lineages BA.1 and BA.2 exhibit enhanced infectivity and a sharp decline in their sensitivity to vaccine-induced neutralizing antibodies. Interestingly, P681 mutations within the viral spike do not play a role in the neutralization potential or infectivity of SARS Cov-2 pseudoviruses carrying mutations in this position. The P681 residue however, dictates the ability of the spike protein to promote fusion and syncytia formation between infected cells. While spike from hCoV-19 (P681) and Omicron (H681) promote only modest cell fusion and formation of syncytia between cells that express the spike-protein, Delta spike (R681) displays enhanced fusogenic activity and promotes syncytia formation. Additional analysis shows that a single P681R mutation within the hCoV-19 spike, or H681R within the Omicron spike, restores fusion potential to similar levels observed for the Delta R681 spike. Conversely, R681P point mutation within the spike of Delta pseudovirus abolishes efficient fusion and syncytia formation. Our investigation also demonstrates that spike proteins from hCoV-19 and Delta SARS-CoV-2 are efficiently incorporated into viral particles relative to the spike of Omicron lineages. We conclude that the third dose of the Pfizer-BNT162b2 provides appreciable protection against the newly emerged Omicron sub-lineages. However, the neutralization sensitivity of these new variants is diminished relative to that of the hCoV-19 or Delta SARS-CoV-2. We further show that the P681 residue within spike dictates cell fusion and syncytia formation with no effects on the infectivity of the specific viral variant and on its sensitivity to vaccine-mediated neutralization.
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Affiliation(s)
- Alona Kuzmina
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
| | - Dina Korovin
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
| | - Ido Cohen Lass
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
| | - Nofar Atari
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel-Hashomer, Israel
| | - Aner Ottolenghi
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
- Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Israel
| | - Pan Hu
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michal Mandelboim
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel-Hashomer, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv, Israel
| | - Benyamin Rosental
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
- Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Israel
| | | | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ran Taube
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
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105
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Zhang F, Jenkins J, de Carvalho RVH, Nakandakari-Higa S, Chen T, Abernathy ME, Baharani VA, Nyakatura EK, Andrew D, Lebedeva IV, Lorenz IC, Hoffmann HH, Rice CM, Victora GD, Barnes CO, Hatziioannou T, Bieniasz PD. Pan-sarbecovirus prophylaxis with human anti-ACE2 monoclonal antibodies. Nat Microbiol 2023; 8:1051-1063. [PMID: 37188812 PMCID: PMC10234812 DOI: 10.1038/s41564-023-01389-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 04/19/2023] [Indexed: 05/17/2023]
Abstract
Human monoclonal antibodies (mAbs) that target the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein have been isolated from convalescent individuals and developed into therapeutics for SARS-CoV-2 infection. However, therapeutic mAbs for SARS-CoV-2 have been rendered obsolete by the emergence of mAb-resistant virus variants. Here we report the generation of a set of six human mAbs that bind the human angiotensin-converting enzyme-2 (hACE2) receptor, rather than the SARS-CoV-2 spike protein. We show that these antibodies block infection by all hACE2 binding sarbecoviruses tested, including SARS-CoV-2 ancestral, Delta and Omicron variants at concentrations of ~7-100 ng ml-1. These antibodies target an hACE2 epitope that binds to the SARS-CoV-2 spike, but they do not inhibit hACE2 enzymatic activity nor do they induce cell-surface depletion of hACE2. They have favourable pharmacology, protect hACE2 knock-in mice against SARS-CoV-2 infection and should present a high genetic barrier to the acquisition of resistance. These antibodies should be useful prophylactic and treatment agents against any current or future SARS-CoV-2 variants and might be useful to treat infection with any hACE2-binding sarbecoviruses that emerge in the future.
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Affiliation(s)
- Fengwen Zhang
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Jesse Jenkins
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | | | | | - Teresia Chen
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Viren A Baharani
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | | | - David Andrew
- Tri-Institutional Therapeutics Discovery Institute, New York, NY, USA
| | - Irina V Lebedeva
- Tri-Institutional Therapeutics Discovery Institute, New York, NY, USA
| | - Ivo C Lorenz
- Tri-Institutional Therapeutics Discovery Institute, New York, NY, USA
| | - H-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Christopher O Barnes
- Department of Biology, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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106
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Picard G, Fournier L, Maisa A, Grolhier C, Chent S, Huchet-Kervalla C, Sudour J, Pretet M, Josset L, Behillil S, Schaeffer J. Emergence, spread and characterisation of the SARS-CoV-2 variant B.1.640 circulating in France, October 2021 to February 2022. Euro Surveill 2023; 28:2200671. [PMID: 37261732 PMCID: PMC10236926 DOI: 10.2807/1560-7917.es.2023.28.22.2200671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/22/2023] [Indexed: 06/02/2023] Open
Abstract
BackgroundSuccessive epidemic waves of COVID-19 illustrated the potential of SARS-CoV-2 variants to reshape the pandemic. Detecting and characterising emerging variants is essential to evaluate their public health impact and guide implementation of adapted control measures.AimTo describe the detection of emerging variant, B.1.640, in France through genomic surveillance and present investigations performed to inform public health decisions.MethodsIdentification and monitoring of SARS-CoV-2 variant B.1.640 was achieved through the French genomic surveillance system, producing 1,009 sequences. Additional investigation of 272 B.1.640-infected cases was performed between October 2021 and January 2022 using a standardised questionnaire and comparing with Omicron variant-infected cases.ResultsB.1.640 was identified in early October 2021 in a school cluster in Bretagne, later spreading throughout France. B.1.640 was detected at low levels at the end of SARS-CoV-2 Delta variant's dominance and progressively disappeared after the emergence of the Omicron (BA.1) variant. A high proportion of investigated B.1.640 cases were children aged under 14 (14%) and people over 60 (27%) years, because of large clusters in these age groups. B.1.640 cases reported previous SARS-CoV-2 infection (4%), anosmia (32%) and ageusia (34%), consistent with data on pre-Omicron SARS-CoV-2 variants. Eight percent of investigated B.1.640 cases were hospitalised, with an overrepresentation of individuals aged over 60 years and with risk factors.ConclusionEven though B.1.640 did not outcompete the Delta variant, its importation and continuous low-level spread raised concerns regarding its public health impact. The investigations informed public health decisions during the time that B.1.640 was circulating.
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Affiliation(s)
- Gwenola Picard
- Bretagne Regional Office, Direction des Régions (DiRe), Santé publique France, Rennes, France
| | - Lucie Fournier
- Direction des Maladies Infectieuses (DMI), Santé publique France, Saint-Maurice, France
| | - Anna Maisa
- Direction des Maladies Infectieuses (DMI), Santé publique France, Saint-Maurice, France
| | - Claire Grolhier
- Department of Virology, INSERM, IRSET UMR-S 1085, Pontchaillou University Hospital, Université de Rennes, Rennes, France
| | - Souhaila Chent
- Hauts-de-France Regional Office, Direction des Régions (DiRe), Santé publique France, Lille, France
| | - Caroline Huchet-Kervalla
- Pays-de-la-Loire Regional Office, Direction des Régions (DiRe), Santé publique France, Nantes, France
| | - Jeanne Sudour
- Direction DATA, Santé publique France, Saint-Maurice, France
| | - Maël Pretet
- Direction DATA, Santé publique France, Saint-Maurice, France
| | - Laurence Josset
- Centre National de Référence Virus des Infections Respiratoires (dont la grippe) and Plateforme GENEPII Laboratoire de Virologie des HCL, Hopital de la Croix Rousse, Lyon, France
- Laboratoire Virpath, CIRI, Inserm U1111, CNRS UMR 5308, ENS de Lyon, UCBL, Lyon, France
| | - Sylvie Behillil
- Unité de Génétique Moléculaire des Virus à ARN - UMR3569 CNRS, Université de Paris, Paris, France
- Centre National de Référence Virus des Infections Respiratoires (dont la grippe), Institut Pasteur, Paris, France
| | - Justine Schaeffer
- Direction des Maladies Infectieuses (DMI), Santé publique France, Saint-Maurice, France
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107
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Pandit R, Matthews QL. A SARS-CoV-2: Companion Animal Transmission and Variants Classification. Pathogens 2023; 12:775. [PMID: 37375465 DOI: 10.3390/pathogens12060775] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
The continuous emergence of novel viruses and their diseases are a threat to global public health as there have been three outbreaks of coronaviruses that are highly pathogenic to humans in the span of the last two decades, severe acute respiratory syndrome (SARS)-CoV in 2002, Middle East respiratory syndrome (MERS)-CoV in 2012, and novel SARS-CoV-2 which emerged in 2019. The unprecedented spread of SARS-CoV-2 worldwide has given rise to multiple SARS-CoV-2 variants that have either altered transmissibility, infectivity, or immune escaping ability, causing diseases in a broad range of animals including human and non-human hosts such as companion, farm, zoo, or wild animals. In this review, we have discussed the recent SARS-CoV-2 outbreak, potential animal reservoirs, and natural infections in companion and farm animals, with a particular focus on SARS-CoV-2 variants. The expeditious development of COVID-19 vaccines and the advancements in antiviral therapeutics have contained the COVID-19 pandemic to some extent; however, extensive research and surveillance concerning viral epidemiology, animal transmission, variants, or seroprevalence in diverse hosts are essential for the future eradication of COVID-19.
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Affiliation(s)
- Rachana Pandit
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
| | - Qiana L Matthews
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
- Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
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108
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Xu K, Sun H, Wang K, Quan Y, Qiao Z, Hu Y, Li C. The Quantification of Spike Proteins in the Inactivated SARS-CoV-2 Vaccines of the Prototype, Delta, and Omicron Variants by LC-MS. Vaccines (Basel) 2023; 11:vaccines11051002. [PMID: 37243106 DOI: 10.3390/vaccines11051002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Developing variant vaccines or multivalent vaccines is a feasible way to address the epidemic as the SARS-CoV-2 variants of concern (VOCs) posed an increased risk to global public health. The spike protein of the SARS-CoV-2 virus was usually used as the main antigen in many types of vaccines to produce neutralizing antibodies against the virus. However, the spike (S) proteins of different variants were only differentiated by a few amino acids, making it difficult to obtain specific antibodies that can distinguish different VOCs, thereby challenging the accurate distinction and quantification of the variants using immunological methods such as ELISA. Here, we established a method based on LC-MS to quantify the S proteins in inactivated monovalent vaccines or trivalent vaccines (prototype, Delta, and Omicron strains). By analyzing the S protein sequences of the prototype, Delta, and Omicron strains, we identified peptides that were different and specific among the three strains and synthesized them as references. The synthetic peptides were isotopically labeled as internal targets. Quantitative analysis was performed by calculating the ratio between the reference and internal target. The verification results have shown that the method we established had good specificity, accuracy, and precision. This method can not only accurately quantify the inactivated monovalent vaccine but also could be applied to each strain in inactivated trivalent SARS-CoV-2 vaccines. Hence, the LC-MS method established in this study can be applied to the quality control of monovalent and multivalent SARS-CoV-2 variation vaccines. By enabling more accurate quantification, it will help to improve the protection of the vaccine to some extent.
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Affiliation(s)
- Kangwei Xu
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China
| | - Huang Sun
- Sinovac Life Sciences Co., Ltd., No. 21, Tianfu St., Daxing Biomedicine Industrial Base of Zhongguancun Science Park, Daxing District, Beijing 100050, China
| | - Kaiqin Wang
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China
| | - Yaru Quan
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China
| | - Zhizhong Qiao
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China
| | - Yaling Hu
- Sinovac Life Sciences Co., Ltd., No. 21, Tianfu St., Daxing Biomedicine Industrial Base of Zhongguancun Science Park, Daxing District, Beijing 100050, China
| | - Changgui Li
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China
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109
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Struble EB, Rawson JMO, Stantchev T, Scott D, Shapiro MA. Uses and Challenges of Antiviral Polyclonal and Monoclonal Antibody Therapies. Pharmaceutics 2023; 15:pharmaceutics15051538. [PMID: 37242780 DOI: 10.3390/pharmaceutics15051538] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Viral diseases represent a major public health concerns and ever-present risks for developing into future pandemics. Antiviral antibody therapeutics, either alone or in combination with other therapies, emerged as valuable preventative and treatment options, including during global emergencies. Here we will discuss polyclonal and monoclonal antiviral antibody therapies, focusing on the unique biochemical and physiological properties that make them well-suited as therapeutic agents. We will describe the methods of antibody characterization and potency assessment throughout development, highlighting similarities and differences between polyclonal and monoclonal products as appropriate. In addition, we will consider the benefits and challenges of antiviral antibodies when used in combination with other antibodies or other types of antiviral therapeutics. Lastly, we will discuss novel approaches to the characterization and development of antiviral antibodies and identify areas that would benefit from additional research.
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Affiliation(s)
- Evi B Struble
- Division of Plasma Derivatives, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Jonathan M O Rawson
- Division of Antivirals, Office of Infectious Diseases, Office of New Drugs, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Tzanko Stantchev
- Division of Biotechnology Review and Research 1, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Dorothy Scott
- Division of Plasma Derivatives, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Marjorie A Shapiro
- Division of Biotechnology Review and Research 1, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
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Baroni C, Potito J, Perticone ME, Orausclio P, Luna CM. How Does Long-COVID Impact Prognosis and the Long-Term Sequelae? Viruses 2023; 15:v15051173. [PMID: 37243259 DOI: 10.3390/v15051173] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/01/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
CONTEXT We reviewed what has been studied and published during the last 3 years about the consequences, mainly respiratory, cardiac, digestive, and neurological/psychiatric (organic and functional), in patients with COVID-19 of prolonged course. OBJECTIVE To conduct a narrative review synthesizing current clinical evidence of abnormalities of signs, symptoms, and complementary studies in COVID-19 patients who presented a prolonged and complicated course. METHODS A review of the literature focused on the involvement of the main organic functions mentioned, based almost exclusively on the systematic search of publications written in English available on PubMed/MEDLINE. RESULTS Long-term respiratory, cardiac, digestive, and neurological/psychiatric dysfunction are present in a significant number of patients. Lung involvement is the most common; cardiovascular involvement may happen with or without symptoms or clinical abnormalities; gastrointestinal compromise includes the loss of appetite, nausea, gastroesophageal reflux, diarrhea, etc.; and neurological/psychiatric compromise can produce a wide variety of signs and symptoms, either organic or functional. Vaccination is not associated with the emergence of long-COVID, but it may happen in vaccinated people. CONCLUSIONS The severity of illness increases the risk of long-COVID. Pulmonary sequelae, cardiomyopathy, the detection of ribonucleic acid in the gastrointestinal tract, and headaches and cognitive impairment may become refractory in severely ill COVID-19 patients.
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Affiliation(s)
- Carolina Baroni
- Department of Medicine, Pulmonary Diseases Division, Hospital de Clínicas, University of Buenos Aires, Buenos Aires C1120 AAF, Argentina
| | - Jorge Potito
- Department of Medicine, Pulmonary Diseases Division, Hospital de Clínicas, University of Buenos Aires, Buenos Aires C1120 AAF, Argentina
| | - María Eugenia Perticone
- Department of Medicine, Pulmonary Diseases Division, Hospital de Clínicas, University of Buenos Aires, Buenos Aires C1120 AAF, Argentina
| | - Paola Orausclio
- Department of Radiology, Centro Rossi, Buenos Aires C1035 ABC, Argentina
| | - Carlos Marcelo Luna
- Department of Medicine, Pulmonary Diseases Division, Hospital de Clínicas, University of Buenos Aires, Buenos Aires C1120 AAF, Argentina
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Wang Z, Li D, Chen Y, Sun Y, Jin C, Hu C, Feng Y, Su J, Ren L, Hao Y, Wang S, Zhu M, Liu Y, Qi J, Zhu B, Shao Y. Characterization of RBD-specific cross-neutralizing antibodies responses against SARS-CoV-2 variants from COVID-19 convalescents. Front Immunol 2023; 14:1160283. [PMID: 37234155 PMCID: PMC10207940 DOI: 10.3389/fimmu.2023.1160283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023] Open
Abstract
Introduction The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been posing a severe threat to global public health. Although broadly neutralizing antibodies have been used to prevent or treat corona virus disease 2019 (COVID-19), new emerging variants have been proven resistant to these antibodies. Methods In this study, we isolated receptor binding domain (RBD)-specific memory B cells using single-cell sorting method from two COVID-19 convalescents and expressed the antibody to test their neutralizing activity against diverse SARS-CoV-2 variants. Then, we resolved antibody-RBD complex structures of potent RBD-specific neutralizing antibodies by X-ray diffraction method. Finally, we analyzed the whole antibody repertoires of the two donors and studied the evolutionary pathway of potent neutralizing antibodies. Results and discussion We identified three potent RBD-specific neutralizing antibodies (1D7, 3G10 and 3C11) from two COVID-19 convalescents that neutralized authentic SARS-CoV-2 WH-1 and Delta variant, and one of them, 1D7, presented broadly neutralizing activity against WH-1, Beta, Gamma, Delta and Omicron authentic viruses. The resolved antibody-RBD complex structures of two antibodies, 3G10 and 3C11, indicate that both of them interact with the external subdomain of the RBD and that they belong to the RBD-1 and RBD-4 communities, respectively. From the antibody repertoire analysis, we found that the CDR3 frequencies of the light chain, which shared high degrees of amino acid identity with these three antibodies, were higher than those of the heavy chain. This research will contribute to the development of RBD-specific antibody-based drugs and immunogens against multiple variants.
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Affiliation(s)
- Zheng Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dan Li
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yulu Chen
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yeping Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Changzhong Jin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Caiqin Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yi Feng
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Junwei Su
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Li Ren
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanling Hao
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shuo Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Meiling Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ying Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Biao Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yiming Shao
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Murugesan M, Raveendran R, Kannangai R, Ramasamy J, Ray P, Gope M, Natarajan V, Walia K, Wattal C, Veeraraghavan B. Indian microbiology EQAS registered laboratory's capacity building and infection control practices during the COVID-19 pandemic in India: Lessons learnt and gaps identified. Indian J Med Microbiol 2023; 43:51-57. [PMID: 36266150 PMCID: PMC9576257 DOI: 10.1016/j.ijmmb.2022.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/03/2022] [Accepted: 09/25/2022] [Indexed: 11/05/2022]
Abstract
PURPOSE The COVID-19 pandemic was unique in the history of outbreaks because of the massive scaling up of resources related to diagnostics, treatment modalities, and vaccines. To understand the impact of the pandemic among laboratory professionals, we aimed to conduct a survey to assess the improvement in the lab capacity post-covid in terms of infrastructure and accreditation status across various levels of hospitals and to determine the changes in the practice of infection control precautions during the pandemic. METHODS This was an anonymous, online-based survey (using 58 item questionnaire) conducted between July 09, 2021, and August 07, 2021. The survey targeted all EQAS registered diagnostic laboratories located in India. RESULTS The survey reached out to 1182 participants, out of which 721 (61%) laboratories completed the questionnaire. During pre-COVID times, only 39% (282/721) of the laboratories had an RT-PCR facility. Among these 721 labs, 514 used open system RT-PCR assay, 217 labs used Truenat assay, 188 labs used GeneXpert assay, 31 used Abbott ID Now and 350 labs performed rapid antigen tests. During the pandemic, 55.3% got NABL accreditation and 7.4% were in the process of applying for COVID-19 molecular testing. In this, 80.7% of the laboratories participated in the ICMR - COVID quality control assessment. It was estimated that 41.4% of the laboratory professionals were re-using N95 masks. Overall, the infection prevention and control practices varied across each laboratory and hospital. CONCLUSION These survey findings helped us to understand the strength and efficiency of laboratories in India in setting up new assays during a crisis time. Based on our findings, we propose to connect this network in a sustained manner to efficiently utilize the existing platforms to adapt to future pandemics.
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Affiliation(s)
- Malathi Murugesan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Reena Raveendran
- Institute of Medical Microbiology and Immunology, Sir Ganga Ram Hospital, New Delhi, India
| | - Rajesh Kannangai
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Jagadish Ramasamy
- Department of Biochemistry, All India Institute of Medical Sciences, Madurai, Tamil Nadu, India
| | - Pallab Ray
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Mallika Gope
- National Accreditation Board for Testing and Calibration Laboratories, Gurugram, Haryana, India
| | - Venkateswaran Natarajan
- National Accreditation Board for Testing and Calibration Laboratories, Gurugram, Haryana, India
| | - Kamini Walia
- Indian Council of Medical Research, New Delhi, India
| | - Chand Wattal
- Institute of Medical Microbiology and Immunology, Sir Ganga Ram Hospital, New Delhi, India.
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India.
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113
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Chiara M, Horner DS, Ferrandi E, Gissi C, Pesole G. HaploCoV: unsupervised classification and rapid detection of novel emerging variants of SARS-CoV-2. Commun Biol 2023; 6:443. [PMID: 37087497 PMCID: PMC10122080 DOI: 10.1038/s42003-023-04784-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 03/30/2023] [Indexed: 04/24/2023] Open
Abstract
Accurate and timely monitoring of the evolution of SARS-CoV-2 is crucial for identifying and tracking potentially more transmissible/virulent viral variants, and implement mitigation strategies to limit their spread. Here we introduce HaploCoV, a novel software framework that enables the exploration of SARS-CoV-2 genomic diversity through space and time, to identify novel emerging viral variants and prioritize variants of potential epidemiological interest in a rapid and unsupervised manner. HaploCoV can integrate with any classification/nomenclature and incorporates an effective scoring system for the prioritization of SARS-CoV-2 variants. By performing retrospective analyses of more than 11.5 M genome sequences we show that HaploCoV demonstrates high levels of accuracy and reproducibility and identifies the large majority of epidemiologically relevant viral variants - as flagged by international health authorities - automatically and with rapid turn-around times.Our results highlight the importance of the application of strategies based on the systematic analysis and integration of regional data for rapid identification of novel, emerging variants of SARS-CoV-2. We believe that the approach outlined in this study will contribute to relevant advances to current and future genomic surveillance methods.
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Affiliation(s)
- Matteo Chiara
- Department of Biosciences, University of Milan, Milan, Italy.
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari, Italy.
| | - David S Horner
- Department of Biosciences, University of Milan, Milan, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Erika Ferrandi
- Department of Biosciences, University of Milan, Milan, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Carmela Gissi
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari, Italy
- Department of Biosciences, Biotechnology and Environment, University of Bari "A. Moro", Bari, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari, Italy.
- Department of Biosciences, Biotechnology and Environment, University of Bari "A. Moro", Bari, Italy.
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Curreli F, Chau K, Tran TT, Nicolau I, Ahmed S, Das P, Hillyer CD, Premenko-Lanier M, Debnath AK. Discovery of Highly Potent Small Molecule Pan-Coronavirus Fusion Inhibitors. Viruses 2023; 15:v15041001. [PMID: 37112982 PMCID: PMC10141620 DOI: 10.3390/v15041001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
The unprecedented pandemic of COVID-19, caused by a novel coronavirus, SARS-CoV-2, and its highly transmissible variants, led to massive human suffering, death, and economic devastation worldwide. Recently, antibody-evasive SARS-CoV-2 subvariants, BQ and XBB, have been reported. Therefore, the continued development of novel drugs with pan-coronavirus inhibition is critical to treat and prevent infection of COVID-19 and any new pandemics that may emerge. We report the discovery of several highly potent small-molecule inhibitors. One of which, NBCoV63, showed low nM potency against SARS-CoV-2 (IC50: 55 nM), SARS-CoV-1 (IC50: 59 nM), and MERS-CoV (IC50: 75 nM) in pseudovirus-based assays with excellent selectivity indices (SI > 900), suggesting its pan-coronavirus inhibition. NBCoV63 showed equally effective antiviral potency against SARS-CoV-2 mutant (D614G) and several variants of concerns (VOCs) such as B.1.617.2 (Delta), B.1.1.529/BA.1 and BA.4/BA.5 (Omicron), and K417T/E484K/N501Y (Gamma). NBCoV63 also showed similar efficacy profiles to Remdesivir against authentic SARS-CoV-2 (Hong Kong strain) and two of its variants (Delta and Omicron), SARS-CoV-1, and MERS-CoV by plaque reduction in Calu-3 cells. Additionally, we show that NBCoV63 inhibits virus-mediated cell-to-cell fusion in a dose-dependent manner. Furthermore, the absorption, distribution, metabolism, and excretion (ADME) data of NBCoV63 demonstrated drug-like properties.
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Affiliation(s)
- Francesca Curreli
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
| | - Kent Chau
- SRI Biosciences (A Division of SRI International), 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
| | - Thanh-Thuy Tran
- SRI Biosciences (A Division of SRI International), 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
| | - Isabella Nicolau
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
| | - Shahad Ahmed
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
| | - Pujita Das
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
| | - Christopher D Hillyer
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
| | - Mary Premenko-Lanier
- SRI Biosciences (A Division of SRI International), 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
- Department of Basic Science, Samuel Merritt University, 3100 Telegraph Avenue, Oakland, CA 94609, USA
| | - Asim K Debnath
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
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115
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Changrob S, Halfmann PJ, Liu H, Torres JL, McGrath JJ, Ozorowski G, Li L, Wilbanks GD, Kuroda M, Maemura T, Huang M, Zheng NY, Turner HL, Erickson SA, Fu Y, Yasuhara A, Singh G, Monahan B, Mauldin J, Srivastava K, Simon V, Krammer F, Sather DN, Ward AB, Wilson IA, Kawaoka Y, Wilson PC. Site of vulnerability on SARS-CoV-2 spike induces broadly protective antibody against antigenically distinct Omicron subvariants. J Clin Invest 2023; 133:e166844. [PMID: 36862518 PMCID: PMC10104900 DOI: 10.1172/jci166844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/28/2023] [Indexed: 03/03/2023] Open
Abstract
The rapid evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants has emphasized the need to identify antibodies with broad neutralizing capabilities to inform future monoclonal therapies and vaccination strategies. Herein, we identified S728-1157, a broadly neutralizing antibody (bnAb) targeting the receptor-binding site (RBS) that was derived from an individual previously infected with WT SARS-CoV-2 prior to the spread of variants of concern (VOCs). S728-1157 demonstrated broad cross-neutralization of all dominant variants, including D614G, Beta, Delta, Kappa, Mu, and Omicron (BA.1/BA.2/BA.2.75/BA.4/BA.5/BL.1/XBB). Furthermore, S728-1157 protected hamsters against in vivo challenges with WT, Delta, and BA.1 viruses. Structural analysis showed that this antibody targets a class 1/RBS-A epitope in the receptor binding domain via multiple hydrophobic and polar interactions with its heavy chain complementarity determining region 3 (CDR-H3), in addition to common motifs in CDR-H1/CDR-H2 of class 1/RBS-A antibodies. Importantly, this epitope was more readily accessible in the open and prefusion state, or in the hexaproline (6P)-stabilized spike constructs, as compared with diproline (2P) constructs. Overall, S728-1157 demonstrates broad therapeutic potential and may inform target-driven vaccine designs against future SARS-CoV-2 variants.
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Affiliation(s)
- Siriruk Changrob
- Drukier Institute for Children’s Health, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - Peter J. Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Jonathan L. Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Joshua J.C. McGrath
- Drukier Institute for Children’s Health, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Lei Li
- Drukier Institute for Children’s Health, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - G. Dewey Wilbanks
- Drukier Institute for Children’s Health, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - Makoto Kuroda
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Tadashi Maemura
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Min Huang
- Drukier Institute for Children’s Health, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - Nai-Ying Zheng
- Drukier Institute for Children’s Health, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - Hannah L. Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Steven A. Erickson
- University of Chicago Department of Medicine, Section of Rheumatology, Chicago, Illinois, USA
| | - Yanbin Fu
- Drukier Institute for Children’s Health, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - Atsuhiro Yasuhara
- Drukier Institute for Children’s Health, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - Gagandeep Singh
- Department of Pathology, Molecular and Cell Based Medicine
- Department of Microbiology
| | - Brian Monahan
- Department of Microbiology
- Center for Vaccine Research and Pandemic Preparedness
| | - Jacob Mauldin
- Department of Microbiology
- Center for Vaccine Research and Pandemic Preparedness
| | - Komal Srivastava
- Department of Microbiology
- Center for Vaccine Research and Pandemic Preparedness
| | - Viviana Simon
- Department of Pathology, Molecular and Cell Based Medicine
- Department of Microbiology
- Center for Vaccine Research and Pandemic Preparedness
- The Global Health and Emerging Pathogens Institute, and
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Florian Krammer
- Department of Pathology, Molecular and Cell Based Medicine
- Department of Microbiology
- Center for Vaccine Research and Pandemic Preparedness
| | - D. Noah Sather
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Pediatrics and
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo, Japan
| | - Patrick C. Wilson
- Drukier Institute for Children’s Health, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
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Ceja-Gálvez HR, Renteria-Flores FI, Nicoletti F, Hernández-Bello J, Macedo-Ojeda G, Muñoz-Valle JF. Severe COVID-19: Drugs and Clinical Trials. J Clin Med 2023; 12:jcm12082893. [PMID: 37109231 PMCID: PMC10142549 DOI: 10.3390/jcm12082893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/08/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
By January of 2023, the COVID-19 pandemic had led to a reported total of 6,700,883 deaths and 662,631,114 cases worldwide. To date, there have been no effective therapies or standardized treatment schemes for this disease; therefore, the search for effective prophylactic and therapeutic strategies is a primary goal that must be addressed. This review aims to provide an analysis of the most efficient and promising therapies and drugs for the prevention and treatment of severe COVID-19, comparing their degree of success, scope, and limitations, with the aim of providing support to health professionals in choosing the best pharmacological approach. An investigation of the most promising and effective treatments against COVID-19 that are currently available was carried out by employing search terms including "Convalescent plasma therapy in COVID-19" or "Viral polymerase inhibitors" and "COVID-19" in the Clinicaltrials.gov and PubMed databases. From the current perspective and with the information available from the various clinical trials assessing the efficacy of different therapeutic options, we conclude that it is necessary to standardize certain variables-such as the viral clearance time, biomarkers associated with severity, hospital stay, requirement of invasive mechanical ventilation, and mortality rate-in order to facilitate verification of the efficacy of such treatments and to better assess the repeatability of the most effective and promising results.
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Affiliation(s)
- Hazael Ramiro Ceja-Gálvez
- Institute of Research in Biomedical Sciences, University Center of Health Sciences (CUCS), University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Francisco Israel Renteria-Flores
- Institute of Research in Biomedical Sciences, University Center of Health Sciences (CUCS), University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Ferdinando Nicoletti
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Jorge Hernández-Bello
- Institute of Research in Biomedical Sciences, University Center of Health Sciences (CUCS), University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Gabriela Macedo-Ojeda
- Institute of Research in Biomedical Sciences, University Center of Health Sciences (CUCS), University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - José Francisco Muñoz-Valle
- Institute of Research in Biomedical Sciences, University Center of Health Sciences (CUCS), University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
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Jaki L, Weigang S, Kern L, Kramme S, Wrobel AG, Grawitz AB, Nawrath P, Martin SR, Dähne T, Beer J, Disch M, Kolb P, Gutbrod L, Reuter S, Warnatz K, Schwemmle M, Gamblin SJ, Neumann-Haefelin E, Schnepf D, Welte T, Kochs G, Huzly D, Panning M, Fuchs J. Total escape of SARS-CoV-2 from dual monoclonal antibody therapy in an immunocompromised patient. Nat Commun 2023; 14:1999. [PMID: 37037847 PMCID: PMC10085998 DOI: 10.1038/s41467-023-37591-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 03/22/2023] [Indexed: 04/12/2023] Open
Abstract
Monoclonal antibodies (mAbs) directed against the spike of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are effective therapeutic options to combat infections in high-risk patients. Here, we report the adaptation of SARS-CoV-2 to the mAb cocktail REGN-COV in a kidney transplant patient with hypogammaglobulinemia. Following mAb treatment, the patient did not clear the infection. During viral persistence, SARS-CoV-2 acquired three novel spike mutations. Neutralization and mouse protection analyses demonstrate a complete viral escape from REGN-COV at the expense of ACE-2 binding. Final clearance of the virus occurred upon reduction of the immunosuppressive regimen and total IgG substitution. Serology suggests that the development of highly neutralizing IgM rather than IgG substitution aids clearance. Our findings emphasise that selection pressure by mAbs on SARS-CoV-2 can lead to development of escape variants in immunocompromised patients. Thus, modification of immunosuppressive therapy, if possible, might be preferable to control and clearance of the viral infection.
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Affiliation(s)
- Lena Jaki
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian Weigang
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lisa Kern
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stefanie Kramme
- Institute for Infection Prevention and Hospital Epidemiology, Freiburg University Medical Center, University of Freiburg, Freiburg, Germany
| | - Antoni G Wrobel
- The Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, UK
| | - Andrea B Grawitz
- Institute for Clinical Chemistry and Laboratory Medicine, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Philipp Nawrath
- The Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, UK
| | - Stephen R Martin
- The Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, UK
| | - Theo Dähne
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julius Beer
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Miriam Disch
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Philipp Kolb
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lisa Gutbrod
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sandra Reuter
- Institute for Infection Prevention and Hospital Epidemiology, Freiburg University Medical Center, University of Freiburg, Freiburg, Germany
| | - Klaus Warnatz
- Department of Rheumatology and Clinical Immunology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martin Schwemmle
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Steven J Gamblin
- The Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, UK
| | - Elke Neumann-Haefelin
- Renal Division, Department of Medicine, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Daniel Schnepf
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thomas Welte
- Renal Division, Department of Medicine, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg Kochs
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Daniela Huzly
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marcus Panning
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Jonas Fuchs
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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Pan YY, Wang LC, Yang F, Yu M. Interferon-lambda: New role in intestinal symptoms of COVID-19. World J Gastroenterol 2023; 29:1942-1954. [PMID: 37155525 PMCID: PMC10122791 DOI: 10.3748/wjg.v29.i13.1942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/25/2022] [Accepted: 03/20/2023] [Indexed: 04/06/2023] Open
Abstract
The tremendous public health and economic impact of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a huge challenge globally. There is increasing evidence that SARS-CoV-2 induces intestinal infections. Type III interferon (IFN-λ) has an antiviral role in intestinal infection, with focused, long-lasting, and non-inflammatory characteristics. This review presents a summary of the structure of SARS-CoV-2, including its invasion and immune escape mechanisms. Emphasis was placed on the gastrointestinal impact of SARS-CoV-2, including changes to the intestinal microbiome, activation of immune cells, and inflammatory responses. We also describe the comprehensive functions of IFN-λ in anti-enteric SARS-CoV-2 infection, and discuss the potential application of IFN-λ as a therapeutic agent for COVID-19 with intestinal symptoms.
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Affiliation(s)
- Yi-Yang Pan
- Department of General Surgery, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Liu-Can Wang
- Department of General Surgery, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Feng Yang
- Department of General Surgery, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Min Yu
- Department of General Surgery, Chongqing General Hospital, Chongqing 400013, China
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119
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Stoddard M, Yuan L, Sarkar S, Mangalaganesh S, Nolan RP, Bottino D, Hather G, Hochberg NS, White LF, Chakravarty A. Heterogeneity in Vaccinal Immunity to SARS-CoV-2 Can Be Addressed by a Personalized Booster Strategy. Vaccines (Basel) 2023; 11:806. [PMID: 37112718 PMCID: PMC10140995 DOI: 10.3390/vaccines11040806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/19/2023] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
SARS-CoV-2 vaccinations were initially shown to substantially reduce risk of severe disease and death. However, pharmacokinetic (PK) waning and rapid viral evolution degrade neutralizing antibody (nAb) binding titers, causing loss of vaccinal protection. Additionally, there is inter-individual heterogeneity in the strength and durability of the vaccinal nAb response. Here, we propose a personalized booster strategy as a potential solution to this problem. Our model-based approach incorporates inter-individual heterogeneity in nAb response to primary SARS-CoV-2 vaccination into a pharmacokinetic/pharmacodynamic (PK/PD) model to project population-level heterogeneity in vaccinal protection. We further examine the impact of evolutionary immune evasion on vaccinal protection over time based on variant fold reduction in nAb potency. Our findings suggest viral evolution will decrease the effectiveness of vaccinal protection against severe disease, especially for individuals with a less durable immune response. More frequent boosting may restore vaccinal protection for individuals with a weaker immune response. Our analysis shows that the ECLIA RBD binding assay strongly predicts neutralization of sequence-matched pseudoviruses. This may be a useful tool for rapidly assessing individual immune protection. Our work suggests vaccinal protection against severe disease is not assured and identifies a potential path forward for reducing risk to immunologically vulnerable individuals.
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Affiliation(s)
| | - Lin Yuan
- Fractal Therapeutics, Lexington, MA 02420, USA
| | - Sharanya Sarkar
- Department of Microbiology and Immunology, Dartmouth College, Hanover, NH 03755, USA
| | - Shruthi Mangalaganesh
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC 3800, Australia
| | | | - Dean Bottino
- Takeda Pharmaceuticals, Cambridge, MA 02139, USA
| | | | - Natasha S. Hochberg
- Department of Epidemiology, Boston University School of Public Health, Boston, MA 02215, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA 02215, USA
- Boston Medical Center, Boston, MA 02118, USA
| | - Laura F. White
- School of Public Health, Boston University, Boston, MA 02118, USA
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120
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Borghi M, Gallinaro A, Pirillo MF, Canitano A, Michelini Z, De Angelis ML, Cecchetti S, Tinari A, Falce C, Mariotti S, Capocefalo A, Chiantore MV, Iacobino A, Di Virgilio A, van Gils MJ, Sanders RW, Lo Presti A, Nisini R, Negri D, Cara A. Different configurations of SARS-CoV-2 spike protein delivered by integrase-defective lentiviral vectors induce persistent functional immune responses, characterized by distinct immunogenicity profiles. Front Immunol 2023; 14:1147953. [PMID: 37090707 PMCID: PMC10113491 DOI: 10.3389/fimmu.2023.1147953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/13/2023] [Indexed: 04/08/2023] Open
Abstract
Several COVID-19 vaccine strategies utilizing new formulations for the induction of neutralizing antibodies (nAbs) and T cell immunity are still under evaluation in preclinical and clinical studies. Here we used Simian Immunodeficiency Virus (SIV)-based integrase defective lentiviral vector (IDLV) delivering different conformations of membrane-tethered Spike protein in the mouse immunogenicity model, with the aim of inducing persistent nAbs against multiple SARS-CoV-2 variants of concern (VoC). Spike modifications included prefusion-stabilizing double proline (2P) substitutions, mutations at the furin cleavage site (FCS), D614G mutation and truncation of the cytoplasmic tail (delta21) of ancestral and Beta (B.1.351) Spike, the latter mutation to markedly improve IDLV membrane-tethering. BALB/c mice were injected once with IDLV delivering the different forms of Spike or the recombinant trimeric Spike protein with 2P substitutions and FCS mutations in association with a squalene-based adjuvant. Anti-receptor binding domain (RBD) binding Abs, nAbs and T cell responses were detected up to six months from a single immunization with escalating doses of vaccines in all mice, but with different levels and kinetics. Results indicated that IDLV delivering the Spike protein with all the combined modifications, outperformed the other candidates in terms of T cell immunity and level of both binding Abs and nAbs soon after the single immunization and persistence over time, showing the best capacity to neutralize all formerly circulating VoC Alpha, Beta, Gamma and Delta. Although present, the lowest response was detected against Omicron variants (BA.1, BA.2 and BA.4/5), suggesting that the magnitude of immune evasion may be related to the higher genetic distance of Omicron as indicated by increased number of amino acid substitutions in Spike acquired during virus evolution.
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Affiliation(s)
- Martina Borghi
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | | | - Andrea Canitano
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Zuleika Michelini
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Laura De Angelis
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Serena Cecchetti
- Confocal Microscopy Unit, Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - Antonella Tinari
- Center for Gender Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Chiara Falce
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Sabrina Mariotti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Antonio Capocefalo
- Department of Veterinary Public Health & Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | | | - Angelo Iacobino
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Antonio Di Virgilio
- Center for Animal Research and Welfare, Istituto Superiore di Sanità, Rome, Italy
| | - Marit J. van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Rogier W. Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | | | - Roberto Nisini
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Donatella Negri
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
- *Correspondence: Donatella Negri, ; Andrea Cara,
| | - Andrea Cara
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
- *Correspondence: Donatella Negri, ; Andrea Cara,
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121
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Shu H, Zhao C, Wang DW. Understanding COVID-19-related myocarditis: pathophysiology, diagnosis, and treatment strategies. CARDIOLOGY PLUS 2023; 8:72-81. [PMID: 37539019 PMCID: PMC10364646 DOI: 10.1097/cp9.0000000000000046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/27/2023] [Indexed: 08/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) disease has infected nearly 600 million people, resulting in > 6 million deaths, with many of them dying from cardiovascular diseases. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is caused by a combination of the virus surface spike protein and the human angiotensin-converting enzyme 2 (ACE2) receptor. In addition to being highly expressed in the lungs, ACE2 is widely distributed in the heart, mainly in myocardial cells and pericytes. Like other types of viruses, SARS-CoV-2 can cause myocarditis after infecting the myocardial tissue, which is attributed to the direct damage of the virus and uncontrolled inflammatory reactions. Patients with chest tightness, palpitation, abnormal electrocardiogram, and cardiac troponin elevation, should be suspected of myocarditis within 1-3 weeks of COVID-19 infection. When the hemodynamics change rapidly, fulminant myocarditis should be suspected. Cardiac ultrasound, myocardial biopsy, cytokine detection, cardiac magnetic resonance imaging, 18F-fluorodeoxyglucose positron emission tomography, and other examination methods can assist in the diagnosis. Although scientists and clinicians have made concerted efforts to seek treatment and prevention measures, there are no clear recommendations for the treatment of COVID-19-related myocarditis. For most cases of common myocarditis, general symptomatic and supportive treatments are used. For COVID-19-related fulminant myocarditis, it is emphasized to achieve "early identification, early diagnosis, early prediction, and early treatment" based on the "life support-based comprehensive treatment regimen." Mechanical circulatory support therapy can rest the heart, which is a cure for symptoms, and immune regulation therapy can control the inflammatory storms which is a cure for the disease. Furthermore, complications of COVID-19-related myocarditis, such as arrhythmia, thrombosis, and infection, should be actively treated. Herein, we summarized the incidence rate, manifestations, and diagnosis of COVID-19-related myocarditis and discussed in detail the treatment of COVID-19-related myocarditis, especially the treatment strategy of fulminant myocarditis.
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Affiliation(s)
- Hongyang Shu
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Chunxia Zhao
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Dao Wen Wang
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
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122
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Zhang H, Jin H, Yan F, Song Y, Dai J, Jiao C, Bai Y, Sun J, Liu D, Wang S, Zhang M, Lu J, Huang J, Huang P, Li Y, Xia X, Wang H. An inactivated recombinant rabies virus chimerically expressed RBD induces humoral and cellular immunity against SARS-CoV-2 and RABV. Virol Sin 2023; 38:244-256. [PMID: 36587795 PMCID: PMC9797420 DOI: 10.1016/j.virs.2022.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/26/2022] [Indexed: 12/30/2022] Open
Abstract
Many studies suggest that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect various animals and transmit among animals, and even to humans, posing a threat to humans and animals. There is an urgent need to develop inexpensive and efficient animal vaccines to prevent and control coronavirus disease 2019 (COVID-19) in animals. Rabies virus (RABV) is another important zoonotic pathogen that infects almost all warm-blooded animals and poses a great public health threat. The present study constructed two recombinant chimeric viruses expressing the S1 and RBD proteins of the SARS-CoV-2 Wuhan01 strain based on a reverse genetic system of the RABV SRV9 strain and evaluated their immunogenicity in mice, cats and dogs. The results showed that both inactivated recombinant viruses induced durable neutralizing antibodies against SARS-CoV-2 and RABV and a strong cellular immune response in mice. Notably, inactivated SRV-nCoV-RBD induced earlier antibody production than SRV-nCoV-S1, which was maintained at high levels for longer periods. Inactivated SRV-nCoV-RBD induced neutralizing antibodies against both SARS-CoV-2 and RABV in cats and dogs, with a relatively broad-spectrum cross-neutralization capability against the SARS-CoV-2 pseudoviruses including Alpha, Beta, Gamma, Delta, and Omicron, showing potential to be used as a safe bivalent vaccine candidate against COVID-19 and rabies in animals.
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Affiliation(s)
- Haili Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Hongli Jin
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China; Changchun Sino Biotechnology Co., Ltd., Changchun, 130012, China
| | - Feihu Yan
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China
| | - Yumeng Song
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Jiaxin Dai
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Cuicui Jiao
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Yujie Bai
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Jingxuan Sun
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Di Liu
- Changchun Sino Biotechnology Co., Ltd., Changchun, 130012, China
| | - Shen Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China
| | - Mengyao Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Jilong Lu
- Changchun Sino Biotechnology Co., Ltd., Changchun, 130012, China
| | - Jingbo Huang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Pei Huang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Yuanyuan Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Xianzhu Xia
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China
| | - Hualei Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
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Kumar R, Srivastava Y, Muthuramalingam P, Singh SK, Verma G, Tiwari S, Tandel N, Beura SK, Panigrahi AR, Maji S, Sharma P, Rai PK, Prajapati DK, Shin H, Tyagi RK. Understanding Mutations in Human SARS-CoV-2 Spike Glycoprotein: A Systematic Review & Meta-Analysis. Viruses 2023; 15:856. [PMID: 37112836 PMCID: PMC10142771 DOI: 10.3390/v15040856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Genetic variant(s) of concern (VoC) of SARS-CoV-2 have been emerging worldwide due to mutations in the gene encoding spike glycoprotein. We performed comprehensive analyses of spike protein mutations in the significant variant clade of SARS-CoV-2, using the data available on the Nextstrain server. We selected various mutations, namely, A222V, N439K, N501Y, L452R, Y453F, E484K, K417N, T478K, L981F, L212I, N856K, T547K, G496S, and Y369C for this study. These mutations were chosen based on their global entropic score, emergence, spread, transmission, and their location in the spike receptor binding domain (RBD). The relative abundance of these mutations was mapped with global mutation D614G as a reference. Our analyses suggest the rapid emergence of newer global mutations alongside D614G, as reported during the recent waves of COVID-19 in various parts of the world. These mutations could be instrumentally imperative for the transmission, infectivity, virulence, and host immune system's evasion of SARS-CoV-2. The probable impact of these mutations on vaccine effectiveness, antigenic diversity, antibody interactions, protein stability, RBD flexibility, and accessibility to human cell receptor ACE2 was studied in silico. Overall, the present study can help researchers to design the next generation of vaccines and biotherapeutics to combat COVID-19 infection.
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Affiliation(s)
- Reetesh Kumar
- Faculty of Agricultural Sciences, Institute of Applied Sciences & Humanities, GLA University, Mathura 281406, India
- Department of Biotherapeutics, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
| | - Yogesh Srivastava
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pandiyan Muthuramalingam
- Division of Horticultural Science, Gyeongsang National University, Jinju 52725, Republic of Korea
| | - Sunil Kumar Singh
- Department of Zoology, School of Biological Sciences, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Geetika Verma
- Department of Biotherapeutics, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
| | - Savitri Tiwari
- Division of Life Sciences, Department of Biosciences, School of Basic and Applied Sciences, Galgotias University, Gautam Buddha Nagar, Greater Noida 201310, India
| | - Nikunj Tandel
- Institute of Science, Nirma University, SG Highway, Gujarat 382481, India
| | - Samir Kumar Beura
- Department of Zoology, School of Biological Sciences, Central University of Punjab, Ghudda, Bathinda 151401, India
| | | | - Somnath Maji
- Department of Radiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Prakriti Sharma
- Biomedical Parasitology and Translational-Immunology Lab, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
| | - Pankaj Kumar Rai
- Department of Biotechnology, IIET, Invertis University, Bareilly 243001, India
| | | | - Hyunsuk Shin
- Division of Horticultural Science, Gyeongsang National University, Jinju 52725, Republic of Korea
| | - Rajeev K. Tyagi
- Biomedical Parasitology and Translational-Immunology Lab, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
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Nizet S, Rieger J, Sarabi A, Lajtai G, Zatloukal K, Tschegg C. Binding and inactivation of human coronaviruses, including SARS-CoV-2, onto purified clinoptilolite-tuff. Sci Rep 2023; 13:4673. [PMID: 36949092 PMCID: PMC10031168 DOI: 10.1038/s41598-023-31744-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/16/2023] [Indexed: 03/24/2023] Open
Abstract
The current COVID19 pandemic is caused by a positive-sense single-stranded RNA virus, which presents high mutational rates. The development of effective therapeutics and mitigation strategies using vaccination or therapeutic antibodies faces serious challenges because of the regular emergence of immune escape variants of the virus. An efficient approach would involve the use of an agent to non-specifically limit or block viruses contacting the mucosae and therefore entering the body. Here, we investigated the ability of a micronized purified clinoptilolite-tuff to bind and neutralize different viruses from the Coronaviridae family. Using plaque assay, RT-qPCR and immunostaining, the adsorption and inactivation of the seasonal human coronavirus HCoV-229E and of 2 SARS-CoV-2 variants were demonstrated. The resulting data suggest that purified clinoptilolite-tuff could be used as an ingredient in new medical devices and/or pharmaceuticals to prevent or mitigate SARS-CoV-2 dissemination.
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Affiliation(s)
- S Nizet
- Glock Health, Science and Research GmbH, Hausfeldstrasse 17, 2232, Deutsch-Wagram, Austria.
| | - J Rieger
- Diagnostic and Research Institute of Pathology, Medical University Graz, Neue Stiftingtalstrasse 6, 8010, Graz, Austria
| | - A Sarabi
- Glock Health, Science and Research GmbH, Hausfeldstrasse 17, 2232, Deutsch-Wagram, Austria
| | | | - K Zatloukal
- Diagnostic and Research Institute of Pathology, Medical University Graz, Neue Stiftingtalstrasse 6, 8010, Graz, Austria
| | - C Tschegg
- Glock Health, Science and Research GmbH, Hausfeldstrasse 17, 2232, Deutsch-Wagram, Austria
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125
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Biggs AT, Littlejohn LF. Describing mRNA Vaccine Technology for a Military Audience. Mil Med 2023; 188:547-554. [PMID: 35584186 DOI: 10.1093/milmed/usac129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/29/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
INTRODUCTION Vaccine technology has improved substantially since the first smallpox vaccine, developed more than 200 years ago. As technology improves, vaccines can be produced more safely and reliably for many different pathogens. A recent breakthrough saw the first full deployment of mRNA vaccines to fight a pandemic. Despite the technological and logistical feat of developing a viable vaccine in an abbreviated time frame, there have been many questions about this new approach to vaccine development. The current review will provide descriptions about different types of vaccines as well as answers to some common questions about mRNA vaccines. The purpose is to provide military medical professionals with the information needed to better convey the importance and function of these new vaccines to service members. MATERIALS AND METHODS There were no explicit inclusion or exclusion criteria for articles describing mRNA vaccine technology. References included here were intended to illustrate important principles or empirical evidence in demonstrating the safety, efficacy, and function of mRNA vaccines. DISCUSSION The review describes three different types of vaccines: whole-pathogen, subunit, and nucleic acid. Each vaccine type has different implications for the development and production of a vaccine line. For example, whole-pathogen and subunit vaccines often require growing significant amounts of the vaccine sample in laboratory before the material can be incorporated into the vaccine. Nucleic acid vaccines instead provide cells the opportunity to produce key proteins without needing to reproduce the virus and attenuate it in a laboratory setting. This approach has a notable advantage of speed in moving from genome sequencing to vaccine production, but it also creates some potential confusion. The discussion covers three questions with regard to this confusion. First, was the vaccine developed too quickly? Speed here is a byproduct of the new technology and unprecedented government interdepartmental cooperation. No steps were skipped in development or production. Second, does the vaccine modify DNA? No, the mRNA vaccines never enter the cell nucleus and therefore cannot modify DNA. The discussion clarifies how mRNA enters cells and produces the key proteins required to stimulate an immune system response. Third, how long will immunity last? Because mRNA vaccines are new, long-term immunity cannot be projected without significant further study. Still, the discussion does cover issues in determining vaccine efficacy in clinical laboratory trials versus field effectiveness in the real world. CONCLUSIONS AND FUTURE USES These mRNA vaccines are the newest and most sophisticated defensive tool military medicine has against emerging biological threats. Evolving dangers, such as synthetic biology and engineered pathogens, further enhance the importance of having defensive countermeasures that can be rapidly deployed in response. Current evidence suggests high safety and effectiveness for a biological countermeasure, decades in the making, and military medical personnel should feel confident using and recommending this technology to ensure force health protection.
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Affiliation(s)
- Adam T Biggs
- Medical Department, Naval Special Warfare Command, Coronado, CA 92155, USA
| | - Lanny F Littlejohn
- Medical Department, Naval Special Warfare Command, Coronado, CA 92155, USA
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Ghoula M, Naceri S, Sitruk S, Flatters D, Moroy G, Camproux AC. Identifying promising druggable binding sites and their flexibility to target the receptor-binding domain of SARS-CoV-2 spike protein. Comput Struct Biotechnol J 2023; 21:2339-2351. [PMID: 36998674 PMCID: PMC10023212 DOI: 10.1016/j.csbj.2023.03.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 03/19/2023] Open
Abstract
The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial for viral infection. The interaction of its receptor-binding domain (RBD) with the human angiotensin-converting enzyme 2 (ACE2) protein is required for the virus to enter the host cell. We identified RBD binding sites to block its function with inhibitors by combining the protein structural flexibility with machine learning analysis. Molecular dynamics simulations were performed on unbound or ACE2-bound RBD conformations. Pockets estimation, tracking and druggability prediction were performed on a large sample of simulated RBD conformations. Recurrent druggable binding sites and their key residues were identified by clustering pockets based on their residue similarity. This protocol successfully identified three druggable sites and their key residues, aiming to target with inhibitors for preventing ACE2 interaction. One site features key residues for direct ACE2 interaction, highlighted using energetic computations, but can be affected by several mutations of the variants of concern. Two highly druggable sites, located between the spike protein monomers interface are promising. One weakly impacted by only one Omicron mutation, could contribute to stabilizing the spike protein in its closed state. The other, currently not affected by mutations, could avoid the activation of the spike protein trimer.
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Affiliation(s)
- M Ghoula
- Université Paris Cité, CNRS, INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - S Naceri
- Université Paris Cité, CNRS, INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - S Sitruk
- Université Paris Cité, CNRS, INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - D Flatters
- Université Paris Cité, CNRS, INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - G Moroy
- Université Paris Cité, CNRS, INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - A C Camproux
- Université Paris Cité, CNRS, INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
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He X, He C, Hong W, Yang J, Wei X. Research progress in spike mutations of SARS-CoV-2 variants and vaccine development. Med Res Rev 2023. [PMID: 36929527 DOI: 10.1002/med.21941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 09/27/2022] [Accepted: 02/26/2023] [Indexed: 03/18/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic can hardly end with the emergence of different variants over time. In the past 2 years, several variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), such as the Delta and Omicron variants, have emerged with higher transmissibility, immune evasion and drug resistance, leading to higher morbidity and mortality in the population. The prevalent variants of concern (VOCs) share several mutations on the spike that can affect virus characteristics, including transmissibility, antigenicity, and immune evasion. Increasing evidence has demonstrated that the neutralization capacity of sera from COVID-19 convalescent or vaccinated individuals is decreased against SARS-CoV-2 variants. Moreover, the vaccine effectiveness of current COVID-19 vaccines against SARS-CoV-2 VOCs is not as high as that against wild-type SARS-CoV-2. Therefore, more attention might be paid to how the mutations impact vaccine effectiveness. In this review, we summarized the current studies on the mutations of the SARS-CoV-2 spike, particularly of the receptor binding domain, to elaborate on how the mutations impact the infectivity, transmissibility and immune evasion of the virus. The effects of mutations in the SARS-CoV-2 spike on the current therapeutics were highlighted, and potential strategies for future vaccine development were suggested.
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Affiliation(s)
- Xuemei He
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Cai He
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Weiqi Hong
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jingyun Yang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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Dadonaite B, Crawford KHD, Radford CE, Farrell AG, Yu TC, Hannon WW, Zhou P, Andrabi R, Burton DR, Liu L, Ho DD, Chu HY, Neher RA, Bloom JD. A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike. Cell 2023; 186:1263-1278.e20. [PMID: 36868218 PMCID: PMC9922669 DOI: 10.1016/j.cell.2023.02.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/11/2023] [Accepted: 01/31/2023] [Indexed: 02/15/2023]
Abstract
A major challenge in understanding SARS-CoV-2 evolution is interpreting the antigenic and functional effects of emerging mutations in the viral spike protein. Here, we describe a deep mutational scanning platform based on non-replicative pseudotyped lentiviruses that directly quantifies how large numbers of spike mutations impact antibody neutralization and pseudovirus infection. We apply this platform to produce libraries of the Omicron BA.1 and Delta spikes. These libraries each contain ∼7,000 distinct amino acid mutations in the context of up to ∼135,000 unique mutation combinations. We use these libraries to map escape mutations from neutralizing antibodies targeting the receptor-binding domain, N-terminal domain, and S2 subunit of spike. Overall, this work establishes a high-throughput and safe approach to measure how ∼105 combinations of mutations affect antibody neutralization and spike-mediated infection. Notably, the platform described here can be extended to the entry proteins of many other viruses.
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Affiliation(s)
- Bernadeta Dadonaite
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Katharine H D Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA 98109, USA
| | - Caelan E Radford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98109, USA
| | - Ariana G Farrell
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Timothy C Yu
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98109, USA
| | - William W Hannon
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98109, USA
| | - Panpan Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, MIT & Harvard, Cambridge, MA 02139, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Helen Y Chu
- University of Washington, Department of Medicine, Division of Allergy and Infectious Diseases, Seattle, WA, USA
| | - Richard A Neher
- Biozentrum, University of Basel, Basel, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
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Joseph J, Darpe S, Kulkarni G, Raj VS. SARS-CoV-2 neutralizing antibody epitopes are overlapping and highly mutated which raises the chances of escape variants and requires development of broadly reactive vaccines. Proteins 2023. [PMID: 36912191 DOI: 10.1002/prot.26488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/07/2023] [Accepted: 02/28/2023] [Indexed: 03/14/2023]
Abstract
The rapid adaptation of SARS-CoV-2 within the host species and the increased viral transmission triggered the evolution of different SARS-CoV-2 variants. Though numerous monoclonal antibodies (mAbs) have been identified as prophylactic therapy for SARS-CoV-2, the ongoing surge in the number of SARS-CoV-2 infections shows the importance of understanding the mutations in the spike and developing novel vaccine strategies to target all variants. Here, we report the map of experimentally validated 74 SARS-CoV-2 neutralizing mAb binding epitopes of all variants. The majority (87.84%) of the potent neutralizing epitopes are localized to the receptor-binding domain (RBD) and overlap with each other, whereas limited (12.16%) epitopes are found in the N-terminal domain (NTD). Notably, 69 out of 74 mAb targets have at least one mutation at the epitope sites. The potent epitopes found in the RBD show higher mutations (4-10aa) compared to lower or modest neutralizing antibodies, suggesting that these epitopes might co-evolve with the immune pressure. The current study shows the importance of determining the critical mutations at the antibody recognition epitopes, leading to the development of broadly reactive immunogens targeting multiple SARS-CoV-2 variants. Further, vaccines inducing both humoral and cell-mediated immune responses might prevent the escape of SARS-CoV-2 variants from neutralizing antibodies.
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Affiliation(s)
- Jeswin Joseph
- Virology Scientific Research (VSR) Laboratory, School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, India
| | - Sukhada Darpe
- Virology Scientific Research (VSR) Laboratory, School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, India
| | - Grishma Kulkarni
- Virology Scientific Research (VSR) Laboratory, School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, India
| | - V Stalin Raj
- Virology Scientific Research (VSR) Laboratory, School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, India
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130
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New insights for infection mechanism and potential targets of COVID-19: Three Chinese patent medicines and three Chinese medicine formulas as promising therapeutic approaches. CHINESE HERBAL MEDICINES 2023; 15:157-168. [PMCID: PMC9993661 DOI: 10.1016/j.chmed.2022.06.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/08/2022] [Accepted: 06/11/2022] [Indexed: 03/11/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with high pathogenicity and infectiousness has become a sudden and lethal pandemic worldwide. Currently, there is no accepted specific drug for COVID-19 treatment. Therefore, it is extremely urgent to clarify the pathogenic mechanism and develop effective therapies for patients with COVID-19. According to several reliable reports from China, traditional Chinese medicine (TCM), especially for three Chinese patent medicines and three Chinese medicine formulas, has been demonstrated to effectively alleviate the symptoms of COVID-19 either used alone or in combination with Western medicines. In this review, we systematically summarized and analyzed the pathogenesis of COVID-19, the detailed clinical practice, active ingredients investigation, network pharmacology prediction and underlying mechanism verification of three Chinese patent medicines and three Chinese medicine formulas in the COVID-19 combat. Additionally, we summarized some promising and high-frequency drugs of these prescriptions and discussed their regulatory mechanism, which provides guidance for the development of new drugs against COVID-19. Collectively, by addressing critical challenges, for example, unclear targets and complicated active ingredients of these medicines and formulas, we believe that TCM will represent promising and efficient strategies for curing COVID-19 and related pandemics.
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Kanteh A, Jallow HS, Manneh J, Sanyang B, Kujabi MA, Ndure SL, Jarju S, Sey AP, Damilare K D, Bah Y, Sambou S, Jarju G, Manjang B, Jagne A, Bittaye SO, Bittaye M, Forrest K, Tiruneh DA, Samateh AL, Jagne S, Hué S, Mohammed N, Amambua-Ngwa A, Kampmann B, D'Alessandro U, de Silva TI, Roca A, Sesay AK. Genomic epidemiology of SARS-CoV-2 infections in The Gambia: an analysis of routinely collected surveillance data between March, 2020, and January, 2022. Lancet Glob Health 2023; 11:e414-e424. [PMID: 36796985 PMCID: PMC9928486 DOI: 10.1016/s2214-109x(22)00553-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 11/30/2022] [Accepted: 12/14/2022] [Indexed: 02/16/2023]
Abstract
BACKGROUND COVID-19, caused by SARS-CoV-2, is one of the deadliest pandemics of the past 100 years. Genomic sequencing has an important role in monitoring of the evolution of the virus, including the detection of new viral variants. We aimed to describe the genomic epidemiology of SARS-CoV-2 infections in The Gambia. METHODS Nasopharyngeal or oropharyngeal swabs collected from people with suspected cases of COVID-19 and international travellers were tested for SARS-CoV-2 with standard RT-PCR methods. SARS-CoV-2-positive samples were sequenced according to standard library preparation and sequencing protocols. Bioinformatic analysis was done using ARTIC pipelines and Pangolin was used to assign lineages. To construct phylogenetic trees, sequences were first stratified into different COVID-19 waves (waves 1-4) and aligned. Clustering analysis was done and phylogenetic trees constructed. FINDINGS Between March, 2020, and January, 2022, 11 911 confirmed cases of COVID-19 were recorded in The Gambia, and 1638 SARS-CoV-2 genomes were sequenced. Cases were broadly distributed into four waves, with more cases during the waves that coincided with the rainy season (July-October). Each wave occurred after the introduction of new viral variants or lineages, or both, generally those already established in Europe or in other African countries. Local transmission was higher during the first and third waves (ie, those that corresponded with the rainy season), in which the B.1.416 lineage and delta (AY.34.1) were dominant, respectively. The second wave was driven by the alpha and eta variants and the B.1.1.420 lineage. The fourth wave was driven by the omicron variant and was predominantly associated with the BA.1.1 lineage. INTERPRETATION More cases of SARS-CoV-2 infection were recorded in The Gambia during peaks of the pandemic that coincided with the rainy season, in line with transmission patterns for other respiratory viruses. The introduction of new lineages or variants preceded epidemic waves, highlighting the importance of implementing well structured genomic surveillance at a national level to detect and monitor emerging and circulating variants. FUNDING Medical Research Unit The Gambia at London School of Hygiene & Tropical Medicine, UK Research and Innovation, WHO.
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Affiliation(s)
- Abdoulie Kanteh
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Haruna S Jallow
- National Public Health Reference Laboratory, Ministry of Health, Banjul, The Gambia
| | - Jarra Manneh
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Bakary Sanyang
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Mariama A Kujabi
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Sainabou Laye Ndure
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Sheikh Jarju
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Alhagie Papa Sey
- National Public Health Reference Laboratory, Ministry of Health, Banjul, The Gambia
| | - Dabiri Damilare K
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Yaya Bah
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | | | | | | | | | | | | | - Karen Forrest
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | | | | | - Sheriffo Jagne
- National Public Health Reference Laboratory, Ministry of Health, Banjul, The Gambia
| | - Stéphane Hué
- Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Nuredin Mohammed
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Alfred Amambua-Ngwa
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Beate Kampmann
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Umberto D'Alessandro
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Thushan I de Silva
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia; The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Anna Roca
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Abdul Karim Sesay
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia.
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Vega R, Antila M, Perez C, Mookadam M, Xie F, Zhang W, Rizwan A, Yao Z, Rasko JE. SARS-CoV-2-neutralising antibody BGB-DXP593 in mild-to-moderate COVID-19: a multicentre, randomised, double-blind, phase 2 trial. EClinicalMedicine 2023; 57:101832. [PMID: 36820098 PMCID: PMC9933486 DOI: 10.1016/j.eclinm.2023.101832] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 12/14/2022] [Accepted: 01/06/2023] [Indexed: 02/18/2023] Open
Abstract
BACKGROUND BGB-DXP593, a neutralising monoclonal antibody against SARS-CoV-2, has demonstrated strong activity in reducing viral RNA copy number in SARS-CoV-2-infected animal models. We aimed to examine the efficacy and safety of BGB-DXP593 in ambulatory patients with mild-to-moderate COVID-19. METHODS This global, randomised, double-blind, phase 2 study (ClinicalTrials.govNCT04551898) screened patients from 20 sites in Australia, Brazil, Mexico, South Africa, and the USA from December 2, 2020, through January 25, 2021. Patients with a first-positive SARS-CoV-2 test (positive reverse transcription-polymerase chain reaction test or authorised antigen test) ≤3 days before screening and mild-to-moderate COVID-19 symptoms for ≤7 days before treatment were randomised 1:1:1:1 to receive a single intravenous infusion of BGB-DXP593 5, 15, or 30 mg/kg, or placebo. The primary endpoint was change from baseline to Day 8 in viral RNA copies/mL as measured in nasopharyngeal swabs. Secondary endpoints were hospitalisation rate due to worsening COVID-19 and treatment-emergent adverse events (TEAEs). A prespecified exploratory endpoint was change in viral RNA copy number in saliva. FINDINGS Relative to the natural rate of clearance as assessed in placebo-exposed patients (-3.12 log10 copies/mL), no significant differences in nasopharygneal viral RNA copy number changes were observed (-2.93 to -3.63 log10 copies/mL) by Day 8 in BGB-DXP593-treated patients. Reductions from baseline to Day 8 in saliva viral RNA copy number were larger with BGB-DXP593 5 mg/kg (-1.37 log10 copies/mL [90% confidence interval -2.14, -0.61]; nominal p = 0.003) and 15 mg/kg (-1.26 [-2.06, -0.46]; nominal p = 0.01) vs placebo, and differences favoring BGB-DXP593 were observed by Day 3, although not statistically significant; no difference from placebo was observed for BGB-DXP593 30 mg/kg (-0.71 [-1.45, 0.04]; nominal p = 0.12). Hospitalisation rate due to COVID-19 was numerically lower with BGB-DXP593 (pooled: 2/134 patients; 1.5%) vs placebo (2/47 patients; 4.3%), although not statistically significant. Incidence of TEAEs was similar across treatment groups. No TEAE led to treatment discontinuation. Five serious TEAEs occurred, all attributed to COVID-19 pneumonia. INTERPRETATION BGB-DXP593 was well tolerated. Although nasopharyngeal swab SARS-CoV-2 viral RNA copy number was not significantly decreased compared with placebo, viral RNA copy number was inconsistently reduced by Day 8 in saliva at some doses as low as 5 mg/kg. FUNDING BeiGene, Ltd.
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Affiliation(s)
- Ramses Vega
- Miami Dade Community Services, Inc., Miami, FL, USA
| | - Martti Antila
- Consultoria Médica e Pesquisa Cliníca, Sorocaba, Brazil
| | - Carlos Perez
- Medical Research Center of Miami II, Miami, FL, USA
| | - Mohamed Mookadam
- Dr Mookadam and Associates, Langeberg Medicross, Cape Town, South Africa
| | | | | | | | - Zhen Yao
- BeiGene (Beijing) Co., Ltd., Beijing, China
| | - John E.J. Rasko
- Gene & Stem Cell Therapy Program, Centenary Institute, and Faculty of Medicine and Health, The University of Sydney, and Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
- Corresponding author. Royal Prince Alfred Hospital, Level 2, Bldg 89, Missenden Rd, Camperdown, NSW, 2050, Australia.
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Hamad M, AlKhamach DMH, Alsayadi LM, Sarhan SA, Saeed BQ, Sokovic M, Ben Hadda T, Soliman SSM. Alpha to Omicron (Variants of Concern): Mutation Journey, Vaccines, and Therapy. Viral Immunol 2023; 36:83-100. [PMID: 36695729 DOI: 10.1089/vim.2022.0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) initially emerged in December 2019 and has subsequently expanded globally, leading to the ongoing pandemic. The extensive spread of various SARS-CoV-2 variants possesses a serious public health threat. An extensive literature search along with deep analysis was performed to describe and evaluate the characteristics of SARS-CoV-2 variants of concern in relation to the effectiveness of the current vaccines and therapeutics. The obtained results showed that several significant mutations have evolved during the COVID-19 pandemic. The developed variants and their various structural mutations can compromise the effectiveness of several vaccines, escape the neutralizing antibodies, and limit the efficiency of available therapeutics. Furthermore, deep analysis of the available data enables the prediction of the future impact of virus mutations on the ongoing pandemic along with the selection of appropriate vaccines and therapeutics.
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Affiliation(s)
- Mohamad Hamad
- College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Dana M H AlKhamach
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | | | | | | | - Marina Sokovic
- Institute for Biological Research "Siniša Stanković," National Institute of the Republic of Serbia, University of Belgrade, Beograd, Serbia
| | - Taibi Ben Hadda
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Sameh S M Soliman
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
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Pushparaj P, Nicoletto A, Castro Dopico X, Sheward DJ, Kim S, Ekström S, Murrell B, Corcoran M, Karlsson Hedestam GB. Frequent use of IGHV3-30-3 in SARS-CoV-2 neutralizing antibody responses. FRONTIERS IN VIROLOGY 2023; 3:1128253. [PMID: 37041983 PMCID: PMC7614418 DOI: 10.3389/fviro.2023.1128253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The antibody response to SARS-CoV-2 shows biased immunoglobulin heavy chain variable (IGHV) gene usage, allowing definition of genetic signatures for some classes of neutralizing antibodies. We investigated IGHV gene usage frequencies by sorting spike-specific single memory B cells from individuals infected with SARS-CoV-2 early in the pandemic. From two study participants and 703 spike-specific B cells, the most used genes were IGHV1-69, IGHV3-30-3, and IGHV3-30. Here, we focused on the IGHV3-30 group of genes and an IGHV3-30-3-using ultrapotent neutralizing monoclonal antibody, CAB-F52, which displayed broad neutralizing activity also in its germline-reverted form. IGHV3-30-3 is encoded by a region of the IGH locus that is highly variable at both the allelic and structural levels. Using personalized IG genotyping, we found that 4 of 14 study participants lacked the IGHV3-30-3 gene on both chromosomes, raising the question if other, highly similar IGHV genes could substitute for IGHV3-30-3 in persons lacking this gene. In the context of CAB-F52, we found that none of the tested IGHV3-33 alleles, but several IGHV3-30 alleles could substitute for IGHV3-30-3, suggesting functional redundancy between the highly homologous IGHV3-30 and IGHV3-30-3 genes for this antibody.
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Affiliation(s)
- Pradeepa Pushparaj
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andrea Nicoletto
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J. Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sungyong Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Simon Ekström
- Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gunilla B. Karlsson Hedestam
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- CORRESPONDENCE Gunilla B. Karlsson Hedestam
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135
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Newby ML, Fogarty CA, Allen JD, Butler J, Fadda E, Crispin M. Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics. J Mol Biol 2023; 435:167928. [PMID: 36565991 PMCID: PMC9769069 DOI: 10.1016/j.jmb.2022.167928] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/25/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
The emergence of SARS-CoV-2 variants alters the efficacy of existing immunity, whether arisen naturally or through vaccination. Understanding the structure of the viral spike assists in determining the impact of mutations on the antigenic surface. One class of mutation impacts glycosylation attachment sites, which have the capacity to influence the antigenic structure beyond the immediate site of attachment. Here, we compare the site-specific glycosylation of recombinant viral spike mimetics of B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta), B.1.1.529 (Omicron). The P.1 strain exhibits two additional N-linked glycan sites compared to the other variants analyzed and we investigate the impact of these glycans by molecular dynamics. The acquired N188 site is shown to exhibit very limited glycan maturation, consistent with limited enzyme accessibility. Structural modeling and molecular dynamics reveal that N188 is located within a cavity by the receptor binding domain, which influences the dynamics of these attachment domains. These observations suggest a mechanism whereby mutations affecting viral glycosylation sites have a structural impact across the protein surface.
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Affiliation(s)
- Maddy L Newby
- School of Biological Sciences, University of Southampton, Southampton, UK. https://twitter.com/Maddy_Newby
| | - Carl A Fogarty
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland. https://twitter.com/2016Carl
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK. https://twitter.com/JoelDalllen
| | - John Butler
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland.
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK.
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136
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Olaiz G, Bertozzi SM, Juárez-Flores A, Borja-Aburto VH, Vicuña F, Ascencio-Montiel IJ, Gutiérrez JP. Evolution of differences in clinical presentation across epidemic waves among patients with COVID-like-symptoms who received care at the Mexican Social Security Institute. Front Public Health 2023; 11:1102498. [PMID: 36923037 PMCID: PMC10009173 DOI: 10.3389/fpubh.2023.1102498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/07/2023] [Indexed: 03/02/2023] Open
Abstract
Background Timely monitoring of SARS-CoV-2 variants is crucial to effectively managing both prevention and treatment efforts. In this paper, we aim to describe demographic and clinical patterns of individuals with COVID-19-like symptoms during the first three epidemic waves in Mexico to identify changes in those patterns that may reflect differences determined by virus variants. Methods We conducted a descriptive analysis of a large database containing records for all individuals who sought care at the Mexican Social Security Institute (IMSS) due to COVID-19-like symptoms from March 2020 to October 2021 (4.48 million records). We described the clinical and demographic profile of individuals tested (3.38 million, 32% with PCR and 68% with rapid test) by test result (positives and negatives) and untested, and among those tested, and the changes in those profiles across the first three epidemic waves. Results Individuals with COVID-19-like symptoms were older in the first wave and younger in the third one (the mean age for those positive was 46.6 in the first wave and 36.1 in the third wave; for negatives and not-tested, the mean age was 41 and 38.5 in the first wave and 34.3 and 33.5 in the third wave). As the pandemic progressed, an increasing number of individuals sought care for suspected COVID-19. The positivity rate decreased over time but remained well over the recommended 5%. The pattern of presenting symptoms changed over time, with some of those symptoms decreasing over time (dyspnea 40.6 to 14.0%, cough 80.4 to 76.2%, fever 77.5 to 65.2%, headache 80.3 to 78.5%), and some increasing (odynophagia 48.7 to 58.5%, rhinorrhea 28.6 to 47.5%, anosmia 11.8 to 23.2%, dysgeusia 11.2 to 23.2%). Conclusion During epidemic surges, the general consensus was that any individual presenting with respiratory symptoms was a suspected COVID-19 case. However, symptoms and signs are dynamic, with clinical patterns changing not only with the evolution of the virus but also with demographic changes in the affected population. A better understanding of these changing patterns is needed to improve preparedness for future surges and pandemics.
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Affiliation(s)
- Gustavo Olaiz
- Center for Policy, Population and Health Research, School of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
| | - Stefano M. Bertozzi
- School of Public Health, University of California, Berkeley, Berkeley, CA, United States
- Department of Global Health, University of Washington, Seattle, WA, United States
- National Institute of Public Health, Mexico (INSP), Cuernavaca, Mexico
| | - Arturo Juárez-Flores
- Center for Policy, Population and Health Research, School of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
| | | | - Félix Vicuña
- Center for Policy, Population and Health Research, School of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
| | - Iván J. Ascencio-Montiel
- Coordination of Epidemiological Surveillance, Mexican Institute of Social Security, Mexico City, Mexico
| | - Juan Pablo Gutiérrez
- Center for Policy, Population and Health Research, School of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
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137
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Assessment of the Biological Impact of SARS-CoV-2 Genetic Variation Using an Authentic Virus Neutralisation Assay with Convalescent Plasma, Vaccinee Sera, and Standard Reagents. Viruses 2023; 15:v15030633. [PMID: 36992342 PMCID: PMC10056478 DOI: 10.3390/v15030633] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
In the summer of 2020, it became clear that the genetic composition of SARS-CoV-2 was changing rapidly. This was highlighted by the rapid emergence of the D614G mutation at that time. In the autumn of 2020, the project entitled “Agility” was initiated with funding from the Coalition for Epidemic Preparedness Innovations (CEPI) to assess new variants of SARS-CoV-2. The project was designed to reach out and intercept swabs containing live variant viruses in order to generate highly characterised master and working stocks, and to assess the biological consequences of the rapid genetic changes using both in vitro and in vivo approaches. Since November 2020, a total of 21 variants have been acquired and tested against either a panel of convalescent sera from early in the pandemic, and/or a panel of plasma from triple-vaccinated participants. A pattern of continuous evolution of SARS-CoV-2 has been revealed. Sequential characterisation of the most globally significant variants available to us, generated in real-time, indicated that the most recent Omicron variants appear to have evolved in a manner that avoids immunological recognition by convalescent plasma from the era of the ancestral virus when analysed in an authentic virus neutralisation assay.
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138
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Boroojerdi MH, Al Jabry T, Mirarefin SMJ, Albalushi H. Insights into organoid-based modeling of COVID-19 pathology. Virol J 2023; 20:37. [PMID: 36841795 PMCID: PMC9959938 DOI: 10.1186/s12985-023-01996-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 02/20/2023] [Indexed: 02/27/2023] Open
Abstract
Since December 2019, various types of strategies have been applied due to the emergent need to investigate the biology and pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to discover a functional treatment. Different disease modeling systems, such as mini-organ technology, have been used to improve our understanding of SARS-CoV-2 physiology and pathology. During the past 2 years, regenerative medicine research has shown the supportive role of organoid modeling in controlling coronavirus disease 2019 (COVID-19) through optimal drug and therapeutic approach improvement. Here, we overview some efforts that have been made to study SARS-CoV-2 by mimicking COVID-19 using stem cells. In addition, we summarize a perspective of drug development in COVID-19 treatment via organoid-based studies.
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Affiliation(s)
- Mohadese Hashem Boroojerdi
- Department of Human and Clinical Anatomy, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Tariq Al Jabry
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | | | - Halima Albalushi
- Department of Human and Clinical Anatomy, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.
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139
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Kumar K, Tan WS, Arshad SS, Ho KL. Virus-like Particles of Nodavirus Displaying the Receptor Binding Domain of SARS-CoV-2 Spike Protein: A Potential VLP-Based COVID-19 Vaccine. Int J Mol Sci 2023; 24:ijms24054398. [PMID: 36901827 PMCID: PMC10001971 DOI: 10.3390/ijms24054398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/06/2023] [Accepted: 02/19/2023] [Indexed: 02/25/2023] Open
Abstract
Since the outbreak of the coronavirus disease 2019 (COVID-19), various vaccines have been developed for emergency use. The efficacy of the initial vaccines based on the ancestral strain of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) has become a point of contention due to the emergence of new variants of concern (VOCs). Therefore, continuous innovation of new vaccines is required to target upcoming VOCs. The receptor binding domain (RBD) of the virus spike (S) glycoprotein has been extensively used in vaccine development due to its role in host cell attachment and penetration. In this study, the RBDs of the Beta (β) and Delta (δ) variants were fused to the truncated Macrobrachium rosenbergii nodavirus capsid protein without the protruding domain (CΔ116-MrNV-CP). Immunization of BALB/c mice with the virus-like particles (VLPs) self-assembled from the recombinant CP showed that, with AddaVax as an adjuvant, a significantly high level of humoral response was elicited. Specifically, mice injected with equimolar of adjuvanted CΔ116-MrNV-CP fused with the RBD of the β- and δ-variants increased T helper (Th) cell production with a CD8+/CD4+ ratio of 0.42. This formulation also induced proliferation of macrophages and lymphocytes. Overall, this study demonstrated that the nodavirus truncated CP fused with the SARS-CoV-2 RBD has potential to be developed as a VLP-based COVID-19 vaccine.
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Affiliation(s)
- Kiven Kumar
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia
| | - Wen Siang Tan
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia
| | - Siti Suri Arshad
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia
- Correspondence: ; Tel.: +603-9769-2729
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140
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Chaguza C, Hahn AM, Petrone ME, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. Cell Rep Med 2023; 4:100943. [PMID: 36791724 PMCID: PMC9906997 DOI: 10.1016/j.xcrm.2023.100943] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/12/2022] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
Abstract
The chronic infection hypothesis for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant emergence is increasingly gaining credence following the appearance of Omicron. Here, we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chronic infection lasting for 471 days (and still ongoing) with consistently recovered infectious virus and high viral genome copies. During the infection, we find an accelerated virus evolutionary rate translating to 35 nucleotide substitutions per year, approximately 2-fold higher than the global SARS-CoV-2 evolutionary rate. This intrahost evolution results in the emergence and persistence of at least three genetically distinct genotypes, suggesting the establishment of spatially structured viral populations continually reseeding different genotypes into the nasopharynx. Finally, we track the temporal dynamics of genetic diversity to identify advantageous mutations and highlight hallmark changes for chronic infection. Our findings demonstrate that untreated chronic infections accelerate SARS-CoV-2 evolution, providing an opportunity for the emergence of genetically divergent variants.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Shuntai Zhou
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David Ferguson
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mario A Peña-Hernández
- Department of Biological and Biomedical Sciences, Yale School of Medicine, New Haven, CT, USA
| | | | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Wade Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Ronald I Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott C Roberts
- Infectious Disease, Yale School of Medicine, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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141
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Tada T, Dcosta BM, Zhou H, Landau NR. Prophylaxis and treatment of SARS-CoV-2 infection by an ACE2 receptor decoy in a preclinical animal model. iScience 2023; 26:106092. [PMID: 36741912 PMCID: PMC9886562 DOI: 10.1016/j.isci.2023.106092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/09/2022] [Accepted: 01/26/2023] [Indexed: 02/01/2023] Open
Abstract
The emergence of SARS-CoV-2 variants with highly mutated spike proteins has presented an obstacle to the use of monoclonal antibodies for the prevention and treatment of SARS-CoV-2 infection. We show that a high-affinity receptor decoy protein in which a modified ACE2 ectodomain is fused to a single domain of an immunoglobulin heavy chain Fc region dramatically suppressed virus loads in mice upon challenge with a high dose of parental SARS-CoV-2 or Omicron variants. The decoy also potently suppressed virus replication when administered shortly post-infection. The decoy approach offers protection against the current viral variants and, potentially, against SARS-CoV-2 variants that may emerge with the continued evolution of the spike protein or novel viruses that use ACE2 for virus entry.
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Affiliation(s)
- Takuya Tada
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, Rm 509, New York, NY 10016, USA
| | - Belinda M. Dcosta
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, Rm 509, New York, NY 10016, USA
| | - Hao Zhou
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, Rm 509, New York, NY 10016, USA
| | - Nathaniel R. Landau
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, Rm 509, New York, NY 10016, USA
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142
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McQuaid C, Solorzano A, Dickerson I, Deane R. Uptake of severe acute respiratory syndrome coronavirus 2 spike protein mediated by angiotensin converting enzyme 2 and ganglioside in human cerebrovascular cells. Front Neurosci 2023; 17:1117845. [PMID: 36875642 PMCID: PMC9980911 DOI: 10.3389/fnins.2023.1117845] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
Introduction There is clinical evidence of neurological manifestations in coronavirus disease-19 (COVID-19). However, it is unclear whether differences in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)/spike protein (SP) uptake by cells of the cerebrovasculature contribute to significant viral uptake to cause these symptoms. Methods Since the initial step in viral invasion is binding/uptake, we used fluorescently labeled wild type and mutant SARS-CoV-2/SP to study this process. Three cerebrovascular cell types were used (endothelial cells, pericytes, and vascular smooth muscle cells), in vitro. Results There was differential SARS-CoV-2/SP uptake by these cell types. Endothelial cells had the least uptake, which may limit SARS-CoV-2 uptake into brain from blood. Uptake was time and concentration dependent, and mediated by angiotensin converting enzyme 2 receptor (ACE2), and ganglioside (mono-sialotetrahexasylganglioside, GM1) that is predominantly expressed in the central nervous system and the cerebrovasculature. SARS-CoV-2/SPs with mutation sites, N501Y, E484K, and D614G, as seen in variants of interest, were also differentially taken up by these cell types. There was greater uptake compared to that of the wild type SARS-CoV-2/SP, but neutralization with anti-ACE2 or anti-GM1 antibodies was less effective. Conclusion The data suggested that in addition to ACE2, gangliosides are also an important entry point of SARS-CoV-2/SP into these cells. Since SARS-CoV-2/SP binding/uptake is the initial step in the viral penetration into cells, a longer exposure and higher titer are required for significant uptake into the normal brain. Gangliosides, including GM1, could be an additional potential SARS-CoV-2 and therapeutic target at the cerebrovasculature.
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Affiliation(s)
| | | | | | - Rashid Deane
- Department of Neuroscience, Del Monte Institute Neuroscience, University of Rochester, University of Rochester Medical Center (URMC), Rochester, NY, United States
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143
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Aguilar R, Li X, Crowell CS, Burrell T, Vidal M, Rubio R, Jiménez A, Hernández-Luis P, Hofmann D, Mijočević H, Jeske S, Christa C, D'Ippolito E, Lingor P, Knolle PA, Roggendorf H, Priller A, Yazici S, Carolis C, Mayor A, Schreiner P, Poppert H, Beyer H, Schambeck SE, Izquierdo L, Tortajada M, Angulo A, Soutschek E, Engel P, Garcia-Basteiro A, Busch DH, Moncunill G, Protzer U, Dobaño C, Gerhard M. RBD-Based ELISA and Luminex Predict Anti-SARS-CoV-2 Surrogate-Neutralizing Activity in Two Longitudinal Cohorts of German and Spanish Health Care Workers. Microbiol Spectr 2023; 11:e0316522. [PMID: 36622140 PMCID: PMC9927417 DOI: 10.1128/spectrum.03165-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/04/2022] [Indexed: 01/10/2023] Open
Abstract
The ability of antibodies to neutralize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important correlate of protection. For routine evaluation of protection, however, a simple and cost-efficient anti-SARS-CoV-2 serological assay predictive of serum neutralizing activity is needed. We analyzed clinical epidemiological data and blood samples from two cohorts of health care workers in Barcelona and Munich to compare several immunological readouts for evaluating antibody levels that could be surrogates of neutralizing activity. We measured IgG levels against SARS-CoV-2 spike protein (S), its S2 subunit, the S1 receptor binding domain (RBD), and the full length and C terminus of nucleocapsid (N) protein by Luminex, and against RBD by enzyme-linked immunosorbent assay (ELISA), and assessed those as predictors of plasma surrogate-neutralizing activity measured by a flow cytometry assay. In addition, we determined the clinical and demographic factors affecting plasma surrogate-neutralizing capacity. Both cohorts showed a high positive correlation between IgG levels to S antigen, especially to RBD, and the levels of plasma surrogate-neutralizing activity, suggesting RBD IgG as a good correlate of plasma neutralizing activity. Symptomatic infection, with symptoms such as loss of taste, dyspnea, rigors, fever and fatigue, was positively associated with anti-RBD IgG positivity by ELISA and Luminex, and with plasma surrogate-neutralizing activity. Our serological assays allow for the prediction of serum neutralization activity without the cost, hazards, time, and expertise needed for surrogate or conventional neutralization assays. Once a cutoff is established, these relatively simple high-throughput antibody assays will provide a fast and cost-effective method of assessing levels of protection from SARS-CoV-2 infection. IMPORTANCE Neutralizing antibody titers are the best correlate of protection against SARS-CoV-2. However, current tests to measure plasma or serum neutralizing activity do not allow high-throughput screening at the population level. Serological tests could be an alternative if they are proved to be good predictors of plasma neutralizing activity. In this study, we analyzed the SARS-CoV-2 serological profiles of two cohorts of health care workers by applying Luminex and ELISA in-house serological assays. Correlations of both serological tests were assessed between them and with a flow cytometry assay to determine plasma surrogate-neutralizing activity. Both assays showed a high positive correlation between IgG levels to S antigens, especially RBD, and the levels of plasma surrogate-neutralizing activity. This result suggests IgG to RBD as a good correlate of plasma surrogate-neutralizing activity and indicates that serology of IgG to RBD could be used to assess levels of protection from SARS-CoV-2 infection.
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Affiliation(s)
- Ruth Aguilar
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Xue Li
- Institute of Medical Microbiology, Immunology, and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Claudia S. Crowell
- Institute of Medical Microbiology, Immunology, and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Teresa Burrell
- Institute of Medical Microbiology, Immunology, and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Marta Vidal
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Rocio Rubio
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Alfons Jiménez
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Pablo Hernández-Luis
- Immunology Unit, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universitat de Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Dieter Hofmann
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Hrvoje Mijočević
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Samuel Jeske
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Catharina Christa
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Elvira D'Ippolito
- Institute of Medical Microbiology, Immunology, and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Paul Lingor
- Klinikum rechts der Isar, Department of Neurology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Percy A. Knolle
- German Center for Infection Research (DZIF), Munich, Germany
- Klinikum rechts der Isar, Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Hedwig Roggendorf
- Klinikum rechts der Isar, Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Alina Priller
- Klinikum rechts der Isar, Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Sarah Yazici
- Klinikum rechts der Isar, Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Carlo Carolis
- Biomolecular Screening and Protein Technologies Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Alfredo Mayor
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | | | | | | | - Sophia E. Schambeck
- Institute of Medical Microbiology, Immunology, and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
- Helios Klinikum München West, Munich, Germany
| | - Luis Izquierdo
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - Marta Tortajada
- Occupational Health Department, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Ana Angulo
- Immunology Unit, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universitat de Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | | | - Pablo Engel
- Immunology Unit, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universitat de Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Alberto Garcia-Basteiro
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
- Department of Preventive Medicine and Epidemiology, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain
| | - Dirk H. Busch
- Institute of Medical Microbiology, Immunology, and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Gemma Moncunill
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - Ulrike Protzer
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Carlota Dobaño
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - Markus Gerhard
- Institute of Medical Microbiology, Immunology, and Hygiene, School of Medicine, Technical University of Munich (TUM), Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
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Olawoye IB, Oluniyi PE, Oguzie JU, Uwanibe JN, Kayode TA, Olumade TJ, Ajogbasile FV, Parker E, Eromon PE, Abechi P, Sobajo TA, Ugwu CA, George UE, Ayoade F, Akano K, Oyejide NE, Nosamiefan I, Fred-Akintunwa I, Adedotun-Sulaiman K, Brimmo FB, Adegboyega BB, Philip C, Adeleke RA, Chukwu GC, Ahmed MI, Ope-Ewe OO, Otitoola SG, Ogunsanya OA, Saibu MF, Sijuwola AE, Ezekiel GO, John OG, Akin-John JO, Akinlo OO, Fayemi OO, Ipaye TO, Nwodo DC, Omoniyi AE, Omwanghe IB, Terkuma CA, Okolie J, Ayo-Ale O, Ikponmwosa O, Benevolence E, Naregose GO, Patience AE, Blessing O, Micheal A, Jacqueline A, Aiyepada JO, Ebhodaghe P, Racheal O, Rita E, Rosemary GE, Solomon E, Anieno E, Edna Y, Chris AO, Donatus AI, Ogbaini-Emovon E, Tatfeng MY, Omunakwe HE, Bob-Manuel M, Ahmed RA, Onwuamah CK, Shaibu JO, Okwuraiwe A, Ataga AE, Bock-Oruma A, Daramola F, Yusuf IF, Fajola A, Ntia NA, Ekpo JJ, Moses AE, Moore-Igwe BW, Fakayode OE, Akinola M, Kida IM, Oderinde BS, Wudiri ZW, Adeyemi OO, Akanbi OA, Ahumibe A, Akinpelu A, Ayansola O, Babatunde O, Omoare AA, Chukwu C, Mba NG, Omoruyi EC, Olisa O, Akande OK, Nwafor IE, Ekeh MA, Ndoma E, Ewah RL, Duruihuoma RO, Abu A, Odeh E, Onyia V, Ojide CK, Okoro S, Igwe D, Ogah EO, Khan K, Ajayi NA, Ugwu CN, Ukwaja KN, Ugwu NI, Abejegah C, Adedosu N, Ayodeji O, Liasu AA, Isamotu RO, Gadzama G, Petros BA, Siddle KJ, Schaffner SF, Akpede G, Erameh CO, Baba MM, Oladiji F, Audu R, Ndodo N, Fowotade A, Okogbenin S, Okokhere PO, Park DJ, Mcannis BL, Adetifa IM, Ihekweazu C, Salako BL, Tomori O, Happi AN, Folarin OA, Andersen KG, Sabeti PC, Happi CT. Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria. Nat Commun 2023; 14:811. [PMID: 36781860 PMCID: PMC9924892 DOI: 10.1038/s41467-023-36449-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 01/26/2023] [Indexed: 02/15/2023] Open
Abstract
Identifying the dissemination patterns and impacts of a virus of economic or health importance during a pandemic is crucial, as it informs the public on policies for containment in order to reduce the spread of the virus. In this study, we integrated genomic and travel data to investigate the emergence and spread of the SARS-CoV-2 B.1.1.318 and B.1.525 (Eta) variants of interest in Nigeria and the wider Africa region. By integrating travel data and phylogeographic reconstructions, we find that these two variants that arose during the second wave in Nigeria emerged from within Africa, with the B.1.525 from Nigeria, and then spread to other parts of the world. Data from this study show how regional connectivity of Nigeria drove the spread of these variants of interest to surrounding countries and those connected by air-traffic. Our findings demonstrate the power of genomic analysis when combined with mobility and epidemiological data to identify the drivers of transmission, as bidirectional transmission within and between African nations are grossly underestimated as seen in our import risk index estimates.
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Affiliation(s)
- Idowu B Olawoye
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Paul E Oluniyi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Judith U Oguzie
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Jessica N Uwanibe
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Tolulope A Kayode
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Testimony J Olumade
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Fehintola V Ajogbasile
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Philomena E Eromon
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Priscilla Abechi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Tope A Sobajo
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Chinedu A Ugwu
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Uwem E George
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Femi Ayoade
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Kazeem Akano
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Nicholas E Oyejide
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Iguosadolo Nosamiefan
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Iyanuoluwa Fred-Akintunwa
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Kemi Adedotun-Sulaiman
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Farida B Brimmo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Babatunde B Adegboyega
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Courage Philip
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Richard A Adeleke
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Grace C Chukwu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Muhammad I Ahmed
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Oludayo O Ope-Ewe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Shobi G Otitoola
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Olusola A Ogunsanya
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Mudasiru F Saibu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Ayotunde E Sijuwola
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Grace O Ezekiel
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Oluwagboadurami G John
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Julie O Akin-John
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Oluwasemilogo O Akinlo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Olanrewaju O Fayemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Testimony O Ipaye
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Deborah C Nwodo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Abolade E Omoniyi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Iyobosa B Omwanghe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Christabel A Terkuma
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Johnson Okolie
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Olubukola Ayo-Ale
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Odia Ikponmwosa
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Ebo Benevolence
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | | | - Osiemi Blessing
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Airende Micheal
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - John O Aiyepada
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - Omiunu Racheal
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Esumeh Rita
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Giwa E Rosemary
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - Ekanem Anieno
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Yerumoh Edna
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Aire O Chris
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | | | - Mirabeau Y Tatfeng
- Department of Medical Laboratory Science, Niger Delta University, Amassoma, Bayelsa State, Nigeria
| | - Hannah E Omunakwe
- Satellite Molecular Laboratory, Rivers State University Teaching Hospital, Port Harcourt, Rivers State, Nigeria
| | - Mienye Bob-Manuel
- Satellite Molecular Laboratory, Rivers State University Teaching Hospital, Port Harcourt, Rivers State, Nigeria
| | - Rahaman A Ahmed
- The Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Chika K Onwuamah
- The Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Joseph O Shaibu
- The Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Azuka Okwuraiwe
- The Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Anthony E Ataga
- Molecular Laboratory, Regional Centre for Biotechnology and Bioresources Research, University of Port Harcourt, Port Harcourt, Rivers State, Nigeria
| | | | - Funmi Daramola
- Clinical Health, SPDC, Port Harcourt, Rivers State, Nigeria
| | | | - Akinwumi Fajola
- Regional Community Health, SPDC, Port Harcourt, Rivers State, Nigeria
| | | | - Julie J Ekpo
- Department of Medical Microbiology and Parasitology, University of Uyo, Uyo, Akwa Ibom State, Nigeria
| | - Anietie E Moses
- Department of Medical Microbiology and Parasitology, University of Uyo, Uyo, Akwa Ibom State, Nigeria
| | | | | | - Monilade Akinola
- WHO Polio Laboratory, University of Maiduguri Teaching Hospital, Maiduguri, Borno State, Nigeria
| | - Ibrahim M Kida
- Department of Immunology, University of Maiduguri Teaching Hospital, Maiduguri, Nigeria
| | - Bamidele S Oderinde
- Department of Immunology, University of Maiduguri Teaching Hospital, Maiduguri, Nigeria
| | - Zara W Wudiri
- Department of Community Medicine, University of Maiduguri Teaching Hospital, Maiduguri, Borno State, Nigeria
| | - Oluwapelumi O Adeyemi
- Department of Medical Microbiology and Parasitology. Faculty of Basic Clinical Sciences. College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | | | | | | | | | | | | | | | - Nwando G Mba
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Ewean C Omoruyi
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Olasunkanmi Olisa
- Biorepository Clinical Virology Laboratory, University of Ibadan, Ibadan, Nigeria
| | - Olatunji K Akande
- Biorepository Clinical Virology Laboratory, University of Ibadan, Ibadan, Nigeria
| | - Ifeanyi E Nwafor
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Matthew A Ekeh
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Erim Ndoma
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Richard L Ewah
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Rosemary O Duruihuoma
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Augustine Abu
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Elizabeth Odeh
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Venatius Onyia
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Chiedozie K Ojide
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Sylvanus Okoro
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Daniel Igwe
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Emeka O Ogah
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Kamran Khan
- Department of Medicine, University of Toronto, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Nnennaya A Ajayi
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Collins N Ugwu
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Kingsley N Ukwaja
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Ngozi I Ugwu
- Haematology Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | | | | | | | | | | | - Galadima Gadzama
- Department of Medical Microbiology, University of Maiduguri Teaching Hospital, Maiduguri, Borno State, Nigeria
| | | | | | | | - George Akpede
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - Marycelin M Baba
- WHO Polio Laboratory, University of Maiduguri Teaching Hospital, Maiduguri, Borno State, Nigeria
- Department of Immunology, University of Maiduguri Teaching Hospital, Maiduguri, Nigeria
| | - Femi Oladiji
- Department of Epidemiology and Community Health, Faculty of Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria
| | - Rosemary Audu
- The Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | | | - Adeola Fowotade
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | | | | | - Danny J Park
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | | | | | | | - Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Anise N Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Onikepe A Folarin
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Christian T Happi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA.
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Ching WY, Adhikari P, Jawad B, Podgornik R. Towards Quantum-Chemical Level Calculations of SARS-CoV-2 Spike Protein Variants of Concern by First Principles Density Functional Theory. Biomedicines 2023; 11:517. [PMID: 36831053 PMCID: PMC9953097 DOI: 10.3390/biomedicines11020517] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
The spike protein (S-protein) is a crucial part of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with its many domains responsible for binding, fusion, and host cell entry. In this review we use the density functional theory (DFT) calculations to analyze the atomic-scale interactions and investigate the consequences of mutations in S-protein domains. We specifically describe the key amino acids and functions of each domain, which are essential for structural stability as well as recognition and fusion processes with the host cell; in addition, we speculate on how mutations affect these properties. Such unprecedented large-scale ab initio calculations, with up to 5000 atoms in the system, are based on the novel concept of amino acid-amino acid-bond pair unit (AABPU) that allows for an alternative description of proteins, providing valuable information on partial charge, interatomic bonding and hydrogen bond (HB) formation. In general, our results show that the S-protein mutations for different variants foster an increased positive partial charge, alter the interatomic interactions, and disrupt the HB networks. We conclude by outlining a roadmap for future computational research of biomolecular virus-related systems.
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Affiliation(s)
- Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA
| | - Puja Adhikari
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA
| | - Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA
- Department of Applied Sciences, University of Technology, Baghdad 10066, Iraq
| | - Rudolf Podgornik
- School of Physical Sciences and Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100090, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
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Umitaibatin R, Harisna AH, Jauhar MM, Syaifie PH, Arda AG, Nugroho DW, Ramadhan D, Mardliyati E, Shalannanda W, Anshori I. Immunoinformatics Study: Multi-Epitope Based Vaccine Design from SARS-CoV-2 Spike Glycoprotein. Vaccines (Basel) 2023; 11:vaccines11020399. [PMID: 36851275 PMCID: PMC9964839 DOI: 10.3390/vaccines11020399] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
The coronavirus disease 2019 outbreak has become a huge challenge in the human sector for the past two years. The coronavirus is capable of mutating at a higher rate than other viruses. Thus, an approach for creating an effective vaccine is still needed to induce antibodies against multiple variants with lower side effects. Currently, there is a lack of research on designing a multiepitope of the COVID-19 spike protein for the Indonesian population with comprehensive immunoinformatic analysis. Therefore, this study aimed to design a multiepitope-based vaccine for the Indonesian population using an immunoinformatic approach. This study was conducted using the SARS-CoV-2 spike glycoprotein sequences from Indonesia that were retrieved from the GISAID database. Three SARS-CoV-2 sequences, with IDs of EIJK-61453, UGM0002, and B.1.1.7 were selected. The CD8+ cytotoxic T-cell lymphocyte (CTL) epitope, CD4+ helper T lymphocyte (HTL) epitope, B-cell epitope, and IFN-γ production were predicted. After modeling the vaccines, molecular docking, molecular dynamics, in silico immune simulations, and plasmid vector design were performed. The designed vaccine is antigenic, non-allergenic, non-toxic, capable of inducing IFN-γ with a population reach of 86.29% in Indonesia, and has good stability during molecular dynamics and immune simulation. Hence, this vaccine model is recommended to be investigated for further study.
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Affiliation(s)
- Ramadhita Umitaibatin
- Lab-on-Chip Group, Department of Biomedical Engineering, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung 40132, Indonesia
| | - Azza Hanif Harisna
- Nano Center Indonesia, Jl. Raya Puspiptek, South Tangerang 15314, Indonesia
| | | | - Putri Hawa Syaifie
- Nano Center Indonesia, Jl. Raya Puspiptek, South Tangerang 15314, Indonesia
| | | | - Dwi Wahyu Nugroho
- Nano Center Indonesia, Jl. Raya Puspiptek, South Tangerang 15314, Indonesia
| | - Donny Ramadhan
- Research Center for Pharmaceutical Ingredients and Traditional Medicine, National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Etik Mardliyati
- Research Center for Vaccine and Drug, National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Wervyan Shalannanda
- Department of Telecommunication Engineering, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung 40132, Indonesia
| | - Isa Anshori
- Lab-on-Chip Group, Department of Biomedical Engineering, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung 40132, Indonesia
- Correspondence:
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Celikgil A, Massimi AB, Nakouzi A, Herrera NG, Morano NC, Lee JH, Yoon HA, Garforth SJ, Almo SC. SARS-CoV-2 multi-antigen protein microarray for detailed characterization of antibody responses in COVID-19 patients. PLoS One 2023; 18:e0276829. [PMID: 36757919 PMCID: PMC9910743 DOI: 10.1371/journal.pone.0276829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/13/2023] [Indexed: 02/10/2023] Open
Abstract
Antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) target multiple epitopes on different domains of the spike protein, and other SARS-CoV-2 proteins. We developed a SARS-CoV-2 multi-antigen protein microarray with the nucleocapsid, spike and its domains (S1, S2), and variants with single (D614G, E484K, N501Y) or double substitutions (N501Y/Deletion69/70), allowing a more detailed high-throughput analysis of the antibody repertoire following infection. The assay was demonstrated to be reliable and comparable to ELISA. We analyzed antibodies from 18 COVID-19 patients and 12 recovered convalescent donors. The S IgG level was higher than N IgG in most of the COVID-19 patients, and the receptor-binding domain of S1 showed high reactivity, but no antibodies were detected against the heptad repeat domain 2 of S2. Furthermore, antibodies were detected against S variants with single and double substitutions in COVID-19 patients who were infected with SARS-CoV-2 early in the pandemic. Here we demonstrated that the SARS-CoV-2 multi-antigen protein microarray is a powerful tool for detailed characterization of antibody responses, with potential utility in understanding the disease progress and assessing current vaccines and therapies against evolving SARS-CoV-2.
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Affiliation(s)
- Alev Celikgil
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Aldo B. Massimi
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Antonio Nakouzi
- Department of Medicine, Division of Infectious Diseases, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Natalia G. Herrera
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Nicholas C. Morano
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - James H. Lee
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Hyun ah Yoon
- Department of Medicine, Division of Infectious Diseases, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, United States of America
| | - Scott J. Garforth
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
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148
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Panahi Y, Gorabi AM, Talaei S, Beiraghdar F, Akbarzadeh A, Tarhriz V, Mellatyar H. An overview on the treatments and prevention against COVID-19. Virol J 2023; 20:23. [PMID: 36755327 PMCID: PMC9906607 DOI: 10.1186/s12985-023-01973-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 01/14/2023] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to plague the world. While COVID-19 is asymptomatic in most individuals, it can cause symptoms like pneumonia, ARDS (acute respiratory distress syndrome), and death in others. Although humans are currently being vaccinated with several COVID-19 candidate vaccines in many countries, however, the world still is relying on hygiene measures, social distancing, and approved drugs. RESULT There are many potential therapeutic agents to pharmacologically fight COVID-19: antiviral molecules, recombinant soluble angiotensin-converting enzyme 2 (ACE2), monoclonal antibodies, vaccines, corticosteroids, interferon therapies, and herbal agents. By an understanding of the SARS-CoV-2 structure and its infection mechanisms, several vaccine candidates are under development and some are currently in various phases of clinical trials. CONCLUSION This review describes potential therapeutic agents, including antiviral agents, biologic agents, anti-inflammatory agents, and herbal agents in the treatment of COVID-19 patients. In addition to reviewing the vaccine candidates that entered phases 4, 3, and 2/3 clinical trials, this review also discusses the various platforms that are used to develop the vaccine COVID-19.
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Affiliation(s)
- Yunes Panahi
- grid.411705.60000 0001 0166 0922Pharmacotherapy Department, Faculty of Pharmacy, Bagyattallah University of Medical Sciences, Tehran, Iran
| | - Armita Mahdavi Gorabi
- grid.411705.60000 0001 0166 0922Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sona Talaei
- grid.449862.50000 0004 0518 4224Department of Basic Sciences, Maragheh University of Medical Sciences, Maragheh, Iran
| | - Fatemeh Beiraghdar
- grid.411521.20000 0000 9975 294XNephrology and Urology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Abolfazl Akbarzadeh
- grid.412888.f0000 0001 2174 8913Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahideh Tarhriz
- grid.412888.f0000 0001 2174 8913Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hassan Mellatyar
- grid.411705.60000 0001 0166 0922Pharmacotherapy Department, Faculty of Pharmacy, Bagyattallah University of Medical Sciences, Tehran, Iran
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149
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Abou-Hamdan M, Saleh R, Mani S, Dournaud P, Metifiot M, Blondot ML, Andreola ML, Abdel-Sater F, De Reggi M, Gressens P, Laforge M. Potential antiviral effects of pantethine against SARS-CoV-2. Sci Rep 2023; 13:2237. [PMID: 36754974 PMCID: PMC9906591 DOI: 10.1038/s41598-023-29245-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 02/01/2023] [Indexed: 02/10/2023] Open
Abstract
SARS-CoV-2 interacts with cellular cholesterol during many stages of its replication cycle. Pantethine was reported to reduce total cholesterol levels and fatty acid synthesis and potentially alter different processes that might be involved in the SARS-CoV-2 replication cycle. Here, we explored the potential antiviral effects of pantethine in two in vitro experimental models of SARS-CoV-2 infection, in Vero E6 cells and in Calu-3a cells. Pantethine reduced the infection of cells by SARS-CoV-2 in both preinfection and postinfection treatment regimens. Accordingly, cellular expression of the viral spike and nucleocapsid proteins was substantially reduced, and we observed a significant reduction in viral copy numbers in the supernatant of cells treated with pantethine. In addition, pantethine inhibited the infection-induced increase in TMPRSS2 and HECT E3 ligase expression in infected cells as well as the increase in antiviral interferon-beta response and inflammatory gene expression in Calu-3a cells. Our results demonstrate that pantethine, which is well tolerated in humans, was very effective in controlling SARS-CoV-2 infection and might represent a new therapeutic drug that can be repurposed for the prevention or treatment of COVID-19 and long COVID syndrome.
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Affiliation(s)
- M Abou-Hamdan
- NeuroDiderot, Inserm, Université Paris Cité, 48 Boulevard Sérurier, 75019, Paris, France.,Biology Department, Faculty of Sciences (I), Lebanese University, Beirut, Lebanon
| | - R Saleh
- NeuroDiderot, Inserm, Université Paris Cité, 48 Boulevard Sérurier, 75019, Paris, France
| | - S Mani
- NeuroDiderot, Inserm, Université Paris Cité, 48 Boulevard Sérurier, 75019, Paris, France
| | - P Dournaud
- NeuroDiderot, Inserm, Université Paris Cité, 48 Boulevard Sérurier, 75019, Paris, France
| | - M Metifiot
- Université Bordeaux, CNRS, UMR 5234, Microbiologie Fondamentale et Pathogénicité, 33076, Bordeaux, France
| | - M L Blondot
- Université Bordeaux, CNRS, UMR 5234, Microbiologie Fondamentale et Pathogénicité, 33076, Bordeaux, France
| | - M L Andreola
- Université Bordeaux, CNRS, UMR 5234, Microbiologie Fondamentale et Pathogénicité, 33076, Bordeaux, France
| | - F Abdel-Sater
- Biochemistry Department, Faculty of Sciences (I), Lebanese University, Beirut, Lebanon
| | - M De Reggi
- NeuroDiderot, Inserm, Université Paris Cité, 48 Boulevard Sérurier, 75019, Paris, France
| | - P Gressens
- NeuroDiderot, Inserm, Université Paris Cité, 48 Boulevard Sérurier, 75019, Paris, France
| | - M Laforge
- NeuroDiderot, Inserm, Université Paris Cité, 48 Boulevard Sérurier, 75019, Paris, France.
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150
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Khatri R, Siddqui G, Sadhu S, Maithil V, Vishwakarma P, Lohiya B, Goswami A, Ahmed S, Awasthi A, Samal S. Intrinsic D614G and P681R/H mutations in SARS-CoV-2 VoCs Alpha, Delta, Omicron and viruses with D614G plus key signature mutations in spike protein alters fusogenicity and infectivity. Med Microbiol Immunol 2023; 212:103-122. [PMID: 36583790 PMCID: PMC9801140 DOI: 10.1007/s00430-022-00760-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 12/03/2022] [Indexed: 12/31/2022]
Abstract
The SARS-CoV-2 virus has been rapidly evolving over the time and the genetic variation has led to the generation of Variants of Concerns (VoC), which have shown increased fitness. These VoC viruses contain the key mutations in the spike protein which have allowed better survival and evasion of host defense mechanisms. The D614G mutation in the spike domain is found in the majority of VoC; additionally, the P681R/H mutation at the S1/S2 furin cleavage site junction is also found to be highly conserved in major VoCs; Alpha, Delta, Omicron, and its' current variants. The impact of these genetic alterations of the SARS-CoV-2 VoCs on the host cell entry, transmissibility, and infectivity has not been clearly identified. In our study, Delta and D614G + P681R synthetic double mutant pseudoviruses showed a significant increase in the cell entry, cell-to-cell fusion and infectivity. In contrast, the Omicron and P681H synthetic single mutant pseudoviruses showed TMPRSS2 independent cell entry, less fusion and infectivity as compared to Delta and D614G + P681R double mutants. Addition of exogenous trypsin further enhanced fusion in Delta viruses as compared to Omicron. Furthermore, Delta viruses showed susceptibility to both E64d and Camostat mesylate inhibitors suggesting, that the Delta virus could exploit both endosomal and TMPRSS2 dependent entry pathways as compared to the Omicron virus. Taken together, these results indicate that the D614G and P681R/H mutations in the spike protein are pivotal which might be favoring the VoC replication in different host compartments, and thus allowing a balance of mutation vs selection for better long-term adaptation.
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Affiliation(s)
- Ritika Khatri
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Gazala Siddqui
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Srikanth Sadhu
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
- Immunobiology and Immunology Core Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Vikas Maithil
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Preeti Vishwakarma
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Bharat Lohiya
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Abhishek Goswami
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Shubbir Ahmed
- Centralized Core Research Facility (CCRF), All India Institute of Medical Science (AIIMS), Delhi, India
| | - Amit Awasthi
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
- Immunobiology and Immunology Core Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Sweety Samal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India.
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