1
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Pérez-Vargas J, Worrall LJ, Olmstead AD, Ton AT, Lee J, Villanueva I, Thompson CAH, Dudek S, Ennis S, Smith JR, Shapira T, De Guzman J, Gang S, Ban F, Vuckovic M, Bielecki M, Kovacic S, Kenward C, Hong CY, Gordon DG, Levett PN, Krajden M, Leduc R, Boudreault PL, Niikura M, Paetzel M, Young RN, Cherkasov A, Strynadka NCJ, Jean F. A novel class of broad-spectrum active-site-directed 3C-like protease inhibitors with nanomolar antiviral activity against highly immune-evasive SARS-CoV-2 Omicron subvariants. Emerg Microbes Infect 2023; 12:2246594. [PMID: 37555275 PMCID: PMC10453993 DOI: 10.1080/22221751.2023.2246594] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/31/2023] [Accepted: 08/06/2023] [Indexed: 08/10/2023]
Abstract
Antivirals with broad coronavirus activity are important for treating high-risk individuals exposed to the constantly evolving SARS-CoV-2 variants of concern (VOCs) as well as emerging drug-resistant variants. We developed and characterized a novel class of active-site-directed 3-chymotrypsin-like protease (3CLpro) inhibitors (C2-C5a). Our lead direct-acting antiviral (DAA), C5a, is a non-covalent, non-peptide with a dissociation constant of 170 nM against recombinant SARS-CoV-2 3CLpro. The compounds C2-C5a exhibit broad-spectrum activity against Omicron subvariants (BA.5, BQ.1.1, and XBB.1.5) and seasonal human coronavirus-229E infection in human cells. Notably, C5a has median effective concentrations of 30-50 nM against BQ.1.1 and XBB.1.5 in two different human cell lines. X-ray crystallography has confirmed the unique binding modes of C2-C5a to the 3CLpro, which can limit virus cross-resistance to emerging Paxlovid-resistant variants. We tested the effect of C5a with two of our newly discovered host-directed antivirals (HDAs): N-0385, a TMPRSS2 inhibitor, and bafilomycin D (BafD), a human vacuolar H+-ATPase [V-ATPase] inhibitor. We demonstrated a synergistic action of C5a in combination with N-0385 and BafD against Omicron BA.5 infection in human Calu-3 lung cells. Our findings underscore that a SARS-CoV-2 multi-targeted treatment for circulating Omicron subvariants based on DAAs (C5a) and HDAs (N-0385 or BafD) can lead to therapeutic benefits by enhancing treatment efficacy. Furthermore, the high-resolution structures of SARS-CoV-2 3CLpro in complex with C2-C5a will facilitate future rational optimization of our novel broad-spectrum active-site-directed 3C-like protease inhibitors.
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Affiliation(s)
- Jimena Pérez-Vargas
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Liam J. Worrall
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - Andrea D. Olmstead
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Anh-Tien Ton
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
| | - Jaeyong Lee
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Ivan Villanueva
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Connor A. H. Thompson
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Svenja Dudek
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Jason R. Smith
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Tirosh Shapira
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Joshua De Guzman
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Shutong Gang
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
| | - Marija Vuckovic
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - Michael Bielecki
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Suzana Kovacic
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Calem Kenward
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - Christopher Yee Hong
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Danielle G. Gordon
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Paul N. Levett
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Mel Krajden
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Richard Leduc
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Canada
| | - Pierre-Luc Boudreault
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Mark Paetzel
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Robert N. Young
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
| | - Natalie C. J. Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - François Jean
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
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2
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Patel A, Kumar S, Lai L, Keen M, Valanparambil R, Chakravarthy C, Laughlin Z, Frank F, Cheedarla N, Verkerke HP, Neish AS, Roback JD, Davis CW, Wrammert J, Sharma A, Ahmed R, Suthar MS, Murali-Krishna K, Chandele A, Ortlund E. Light chain of a public SARS-CoV-2 class-3 antibody modulates neutralization against Omicron. Cell Rep 2023; 42:113150. [PMID: 37708028 PMCID: PMC10862350 DOI: 10.1016/j.celrep.2023.113150] [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: 05/24/2023] [Revised: 08/14/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023] Open
Abstract
The pairing of antibody genes IGHV2-5/IGLV2-14 is established as a public immune response that potently cross-neutralizes SARS-CoV-2 variants, including Omicron, by targeting class-3/RBD-5 epitopes in the receptor binding domain (RBD). LY-CoV1404 (bebtelovimab) exemplifies this, displaying exceptional potency against Omicron sub-variants up to BA.5. Here, we report a human antibody, 002-S21B10, encoded by the public clonotype IGHV2-5/IGLV2-14. While 002-S21B10 neutralized key SARS-CoV-2 variants, it did not neutralize Omicron, despite sharing >92% sequence similarity with LY-CoV1404. The structure of 002-S21B10 in complex with spike trimer plus structural and sequence comparisons with LY-CoV1404 and other IGHV2-5/IGLV2-14 antibodies revealed significant variations in light-chain orientation, paratope residues, and epitope-paratope interactions that enable some antibodies to neutralize Omicron but not others. Confirming this, replacing the light chain of 002-S21B10 with the light chain of LY-CoV1404 restored 002-S21B10's binding to Omicron. Understanding such Omicron evasion from public response is vital for guiding therapeutics and vaccine design.
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Affiliation(s)
- Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sanjeev Kumar
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India; Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Lilin Lai
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Meredith Keen
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Rajesh Valanparambil
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Chennareddy Chakravarthy
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Zane Laughlin
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Filipp Frank
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hans P Verkerke
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Andrew S Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John D Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Carl W Davis
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Jens Wrammert
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Amit Sharma
- Structural Parasitology Group, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Rafi Ahmed
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Mehul S Suthar
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Kaja Murali-Krishna
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India; Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA.
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India.
| | - Eric Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.
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3
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Islam MJ, Alom MS, Hossain MS, Ali MA, Akter S, Islam S, Ullah MO, Halim MA. Unraveling the impact of ORF3a Q57H mutation on SARS-CoV-2: insights from molecular dynamics. J Biomol Struct Dyn 2023:1-14. [PMID: 37649361 DOI: 10.1080/07391102.2023.2252908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
ORF3a is a conserved accessory protein of SARS-CoV-2, linked to viral infection and pathogenesis, with acquired mutations at various locations. Previous studies have shown that the occurrence of the Q57H mutation is higher in comparison to other positions in ORF3a. This mutation is known to induce conformational changes, yet the extent of structural alteration and its role in the viral adaptation process remain unknown. Here we performed molecular dynamics (MD) simulations of wt-ORF3a, Q57H, and Q57A mutants to analyze structural changes caused by mutations compared to the native protein. The MD analysis revealed that Q57H and Q57A mutants show significant structural changes in the dimer conformation than the wt-ORF3a. This dimer conformer narrows down the ion channel cavity, which reduces Na + or K + permeability leading to decrease the antigenic response that can help the virus to escape the host immune system. Non-bonding interaction analysis shows the Q57H mutant has more interacting residues, resulting in more stability within dimer conformation than the wt-ORF3a and Q57A. Moreover, both mutant dimers (Q57H and Q57A) form a novel salt-bridge interaction at the same position between A:Asp142 and B:Lys61, whereas such an interaction is absent in the wt-ORF3a dimer. We have also noticed that the TM3 domain's flexibility in Q57H is increased because of strong inter-domain interactions of TM1 and TM2 within the dimer conformation. These unusual interactions and flexibility of Q57H mutant can have significant impacts on the SARS-CoV-2 adaptations, virulence, transmission, and immune system evasion. Our findings are consistent with the previous experimental data and provided details information on the structural perturbation in ORF3a caused by mutations, which can help better understand the structural change at the molecular level as well as the reason for the high virulence properties of this variant.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Jahirul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Md Siddik Alom
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Md Shahadat Hossain
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Md Ackas Ali
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, USA
| | - Shaila Akter
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Shafiqul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - M Obayed Ullah
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Mohammad A Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, USA
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4
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Lubin JH, Markosian C, Balamurugan D, Ma MT, Chen CH, Liu D, Pasqualini R, Arap W, Burley SK, Khare SD. Modeling of ACE2 and antibodies bound to SARS-CoV-2 provides insights into infectivity and immune evasion. JCI Insight 2023; 8:e168296. [PMID: 37261904 PMCID: PMC10371346 DOI: 10.1172/jci.insight.168296] [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: 12/23/2022] [Accepted: 05/26/2023] [Indexed: 06/03/2023] Open
Abstract
Given the COVID-19 pandemic, there is interest in understanding ligand-receptor features and targeted antibody-binding attributes against emerging SARS-CoV-2 variants. Here, we developed a large-scale structure-based pipeline for analysis of protein-protein interactions regulating SARS-CoV-2 immune evasion. First, we generated computed structural models of the Spike protein of 3 SARS-CoV-2 variants (B.1.1.529, BA.2.12.1, and BA.5) bound either to a native receptor (ACE2) or to a large panel of targeted ligands (n = 282), which included neutralizing or therapeutic monoclonal antibodies. Moreover, by using the Barnes classification, we noted an overall loss of interfacial interactions (with gain of new interactions in certain cases) at the receptor-binding domain (RBD) mediated by substituted residues for neutralizing complexes in classes 1 and 2, whereas less destabilization was observed for classes 3 and 4. Finally, an experimental validation of predicted weakened therapeutic antibody binding was performed in a cell-based assay. Compared with the original Omicron variant (B.1.1.529), derivative variants featured progressive destabilization of antibody-RBD interfaces mediated by a larger set of substituted residues, thereby providing a molecular basis for immune evasion. This approach and findings provide a framework for rapidly and efficiently generating structural models for SARS-CoV-2 variants bound to ligands of mechanistic and therapeutic value.
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Affiliation(s)
- Joseph H. Lubin
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Christopher Markosian
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey, USA
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - D. Balamurugan
- Office of Advanced Research Computing, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Department of Radiology
| | - Minh T. Ma
- Department of Pathology, Immunology, and Laboratory Medicine
- Center for Immunity and Inflammation, and
| | - Chih-Hsiung Chen
- Department of Pathology, Immunology, and Laboratory Medicine
- Center for Immunity and Inflammation, and
| | - Dongfang Liu
- Department of Pathology, Immunology, and Laboratory Medicine
- Center for Immunity and Inflammation, and
| | - Renata Pasqualini
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey, USA
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Wadih Arap
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey, USA
- Division of Hematology/Oncology, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Stephen K. Burley
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- RCSB Protein Data Bank, San Diego Supercomputer Center, UCSD, La Jolla, California, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Sagar D. Khare
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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5
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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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6
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Mahita J, Ha B, Gambiez A, Schendel SL, Li H, Hastie KM, Dennison SM, Li K, Kuzmina N, Periasamy S, Bukreyev A, Munt JE, Osei-Twum M, Atyeo C, Overton JA, Vita R, Guzman-Orozco H, Mendes M, Kojima M, Halfmann PJ, Kawaoka Y, Alter G, Gagnon L, Baric RS, Tomaras GD, Germann T, Bedinger D, Greenbaum JA, Saphire EO, Peters B. Coronavirus Immunotherapeutic Consortium Database. Database (Oxford) 2023; 2023:7034146. [PMID: 36763096 PMCID: PMC9913043 DOI: 10.1093/database/baac112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/30/2022] [Accepted: 12/22/2022] [Indexed: 02/11/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has seen multiple anti-SARS-CoV-2 antibodies being generated globally. It is difficult, however, to assemble a useful compendium of these biological properties if they are derived from experimental measurements performed at different sites under different experimental conditions. The Coronavirus Immunotherapeutic Consortium (COVIC) circumvents these issues by experimentally testing blinded antibodies side by side for several functional activities. To collect these data in a consistent fashion and make it publicly available, we established the COVIC database (COVIC-DB, https://covicdb.lji.org/). This database enables systematic analysis and interpretation of this large-scale dataset by providing a comprehensive view of various features such as affinity, neutralization, in vivo protection and effector functions for each antibody. Interactive graphs enable direct comparisons of antibodies based on select functional properties. We demonstrate how the COVIC-DB can be utilized to examine relationships among antibody features, thereby guiding the design of therapeutic antibody cocktails. Database URL https://covicdb.lji.org/.
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Affiliation(s)
| | | | - Anais Gambiez
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Sharon L Schendel
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Haoyang Li
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Kathryn M Hastie
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - S Moses Dennison
- Center for Human Systems Immunology, Departments of Surgery, Immunology, and Molecular Genetics and Microbiology and Duke Human Vaccine Institute, Duke University, Durham, NC 27701, USA
| | - Kan Li
- Center for Human Systems Immunology, Departments of Surgery, Immunology, and Molecular Genetics and Microbiology and Duke Human Vaccine Institute, Duke University, Durham, NC 27701, USA
| | - Natalia Kuzmina
- Department of Pathology, University of Texas Medical Branch at Galveston, 301 University Blvd, Galveston, TX 77555-0609, USA,Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, 301 University Blvd, Galveston, TX 77555-1019, USA
| | - Sivakumar Periasamy
- Department of Pathology, University of Texas Medical Branch at Galveston, 301 University Blvd, Galveston, TX 77555-0609, USA,Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, 301 University Blvd, Galveston, TX 77555-1019, USA
| | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch at Galveston, 301 University Blvd, Galveston, TX 77555-0609, USA,Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, 301 University Blvd, Galveston, TX 77555-1019, USA,Galveston National Laboratory, University of Texas Medical Branch at Galveston, 301 University Blvd, Galveston, TX 77550, USA
| | - Jennifer E Munt
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, 135 Dauer Drive, 2101 McGavran-Greenberg Hall,CB #7435, Chapel Hill, NC 27599-7435, USA
| | - Mary Osei-Twum
- Nexelis, a Q2 Solutions Company, 525 Boulevard Cartier Ouest, Laval, Quebec H7V 3S8, Canada
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT and Harvard, 400 Technology Square, Cambrige, MA 02139-3583, USA
| | - James A Overton
- Knocean Inc., 107 Quebec Ave. Toronto, Ontario, M6P 2T3, Canada
| | - Randi Vita
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Hector Guzman-Orozco
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Marcus Mendes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Mari Kojima
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, WI 53711, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, WI 53711, USA,Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan,The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, 400 Technology Square, Cambrige, MA 02139-3583, USA
| | - Luc Gagnon
- Nexelis, a Q2 Solutions Company, 525 Boulevard Cartier Ouest, Laval, Quebec H7V 3S8, Canada
| | - Ralph S Baric
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, 135 Dauer Drive, 2101 McGavran-Greenberg Hall,CB #7435, Chapel Hill, NC 27599-7435, USA,Department of Microbiology and Immunology, School of Medicine, 125 Marson Farm Road, Chapel Hill, NC 27599-7290, USA
| | - Georgia D Tomaras
- Center for Human Systems Immunology, Departments of Surgery, Immunology, and Molecular Genetics and Microbiology and Duke Human Vaccine Institute, Duke University, Durham, NC 27701, USA
| | - Tim Germann
- Carterra Inc., 825 N. 300 W.Ste, C309, Salt Lake City, UT 84103, USA
| | - Daniel Bedinger
- Carterra Inc., 825 N. 300 W.Ste, C309, Salt Lake City, UT 84103, USA
| | - Jason A Greenbaum
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | | | - Bjoern Peters
- Correspondence may also be addressed to Bjoern Peters. Tel: +1858 752 6914; Fax: +858-752-6987;
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7
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Structural patterns of SARS-CoV-2 variants of concern (alpha, beta, gamma, delta) spike protein are influenced by variant-specific amino acid mutations: A computational study with implications on viral evolution. J Theor Biol 2023; 558:111376. [PMID: 36473508 PMCID: PMC9721161 DOI: 10.1016/j.jtbi.2022.111376] [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: 06/03/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 (SARS2) regularly mutates resulting to variants of concern (VOC) which have higher virulence and transmissibility rates while concurrently evading available therapeutic strategies. This highlights the importance of amino acid mutations occurring in the SARS2 spike protein structure since it may affect virus biology. However, this was never fully elucidated. Here, network analysis was performed based on the COVID-19 genomic epidemiology network between December 2019-July 2021. Representative SARS2 VOC spike protein models were generated and quality checked, protein model superimposition was done, and common contact based on contact mapping was established. Throughout this study, we found that: (1) certain individual variant-specific amino acid mutations can affect the spike protein structural pattern; (2) certain individual variant-specific amino acid mutations had no affect on the spike protein structural pattern; and (3) certain combination of variant-specific amino acids are putatively epistatic mutations that can potentially influence the VOC spike protein structural pattern. This manuscript was submitted as part of a theme issue on "Modelling COVID-19 and Preparedness for Future Pandemics".
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8
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Salimović-Bešić I, Dedeić-Ljubović A, Zahirović E, Hasanović M, Šehić M, Vukovikj M, Boshevska G, Vegar-Zubović S, Mehmedika-Suljić E, Izetbegović S. The SARS-CoV-2 Delta (B.1.617.2) variant with spike N501Y mutation in the shadow of Omicron emergence. Heliyon 2022; 8:e12650. [PMID: 36590492 PMCID: PMC9789543 DOI: 10.1016/j.heliyon.2022.e12650] [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: 04/05/2022] [Revised: 10/05/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
Circulation of the Omicron variant with the reemergence of the N501Y mutation along with many others in the spike protein has once again stirred the academic community. Interestingly, tracing the genetic diversity of SARS-CoV-2 shed light on a less frequent N501Y + Delta variant which has been in the global circulation for some time before the Omicron appearance. This paper aims to present the molecular characteristics of the SARS-CoV-2 Spike_N501Y + Delta variant detected in Bosnia and Herzegovina. The study was conducted during November and December 2021. All patients were tested using real-time RT-PCR for detection of SARS-CoV-2. A representative number of SARS-CoV-2 positive samples was pre-screened using VirSNiP SARS-CoV-2 Spike N501Y kit. The characterization of the viruses was carried out with Illumina RNA Prep with enrichment and the Respiratory Virus Oligo Panel kit. Among the analyzed sequences, we found two isolates of the Delta variant that differ from their most related clade- GK AY.4.3 in additional mutations N501Y and L54F. In this study, we described the presence of a rare form of Delta variant with Spike_N501Y mutation in the shadow of the Omicron emergence. Despite the set of mutations in the Spike protein, this form of Delta variant does not indicate the large-scale consequences for the general population. Further functional studies of this form could provide more information about its antigenicity and infectivity.
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Affiliation(s)
- Irma Salimović-Bešić
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina,Corresponding author.
| | - Amela Dedeić-Ljubović
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
| | - Edina Zahirović
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
| | - Medina Hasanović
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
| | - Merima Šehić
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
| | - Maja Vukovikj
- Institute of Public Health of Republic of North Macedonia, 50-ta Divizija 6, 1000, Skopje, Macedonia
| | - Golubinka Boshevska
- Faculty for Medical Sciences, University Goce Delchev, Krste Misirkov No.10-A P.O. Box 201, 2000, Shtip, Macedonia
| | - Sandra Vegar-Zubović
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
| | - Enra Mehmedika-Suljić
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
| | - Sebija Izetbegović
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
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9
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Arikan A, Sayan M. Investigation of SARS-CoV-2 Variants and Their Effect on SARS-CoV-2 Monoclonal Antibodies, Convalescent and Vaccine Plasma by a Novel Web Tool. Diagnostics (Basel) 2022; 12:diagnostics12112869. [PMID: 36428929 PMCID: PMC9689196 DOI: 10.3390/diagnostics12112869] [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: 10/03/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
(1) Background: SARS-CoV-2 variants possess specific mutations throughout their genome; however, the effect of these mutations on pathogenesis is little known. The study aimed to identify SARS-CoV-2 variants and their susceptibility rate against monoclonal antibodies, convalescent, and vaccine plasma. (2) Methods: Strains isolated from COVID-19 cases in Turkey in April and September 2021 were involved. Illuma Nextera XT was processed for NGS, followed by virtual phenotyping (Coronavirus Antiviral and Resistance Database (CoV-RDB) by Stanford University). (3) Results: Among 211 strains, 79% were SARS-CoV-2 variants. B.1.1.7 (Alpha) was the most dominant, followed by B.1.617.2 (Delta), B.1.351 (Beta), and B.1.525 (Eta). Alpha and Delta were less susceptible to Etesevimab-Sotrovimab and Bamlanivimab-Etesevimab, respectively. Reduced efficacy was observed for convalescent plasma in Beta and Delta; AstraZeneca, Comirnaty plus AstraZeneca in Alpha; Comirnaty, Moderna, Novovax in Beta; Comirnaty in Delta. (4) Conclusion: CoV-RDB analysis is an efficient, rapid, and helpful web tool for SARS-CoV-2 variant detection and susceptibility analysis.
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Affiliation(s)
- Ayse Arikan
- Department of Medical Microbiology and Clinical Microbiology, Faculty of Medicine, Near East University, Nicosia 99138, Northern Cyprus, Turkey
- DESAM Research Institute, Near East University, Nicosia 99138, Northern Cyprus, Turkey
- Department of Medical Microbiology and Clinical Microbiology, Faculty of Medicine, Kyrenia University, Kyrenia 99320, Northern Cyprus, Turkey
- Correspondence:
| | - Murat Sayan
- DESAM Research Institute, Near East University, Nicosia 99138, Northern Cyprus, Turkey
- PCR Unit, Research and Education Hospital, Kocaeli University, Izmit 41380, Kocaeli, Turkey
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10
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Taft JM, Weber CR, Gao B, Ehling RA, Han J, Frei L, Metcalfe SW, Overath MD, Yermanos A, Kelton W, Reddy ST. Deep mutational learning predicts ACE2 binding and antibody escape to combinatorial mutations in the SARS-CoV-2 receptor-binding domain. Cell 2022; 185:4008-4022.e14. [PMID: 36150393 PMCID: PMC9428596 DOI: 10.1016/j.cell.2022.08.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 06/22/2022] [Accepted: 08/25/2022] [Indexed: 01/26/2023]
Abstract
The continual evolution of SARS-CoV-2 and the emergence of variants that show resistance to vaccines and neutralizing antibodies threaten to prolong the COVID-19 pandemic. Selection and emergence of SARS-CoV-2 variants are driven in part by mutations within the viral spike protein and in particular the ACE2 receptor-binding domain (RBD), a primary target site for neutralizing antibodies. Here, we develop deep mutational learning (DML), a machine-learning-guided protein engineering technology, which is used to investigate a massive sequence space of combinatorial mutations, representing billions of RBD variants, by accurately predicting their impact on ACE2 binding and antibody escape. A highly diverse landscape of possible SARS-CoV-2 variants is identified that could emerge from a multitude of evolutionary trajectories. DML may be used for predictive profiling on current and prospective variants, including highly mutated variants such as Omicron, thus guiding the development of therapeutic antibody treatments and vaccines for COVID-19.
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Affiliation(s)
- Joseph M. Taft
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland,Botnar Research Centre for Child Health, Basel 4058, Switzerland
| | - Cédric R. Weber
- Alloy Therapeutics (Switzerland) AG, Basel 4058, Switzerland
| | - Beichen Gao
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland,Botnar Research Centre for Child Health, Basel 4058, Switzerland
| | - Roy A. Ehling
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Jiami Han
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland,Botnar Research Centre for Child Health, Basel 4058, Switzerland
| | - Lester Frei
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland,Botnar Research Centre for Child Health, Basel 4058, Switzerland
| | - Sean W. Metcalfe
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Max D. Overath
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland,Botnar Research Centre for Child Health, Basel 4058, Switzerland,Department of Biology, Institute of Microbiology and Immunology, ETH Zurich, Zurich 8093, Switzerland,Department of Pathology and Immunology, University of Geneva, Geneva 1211, Switzerland
| | - William Kelton
- Te Huataki Waiora School of Health, University of Waikato, Hamilton 3240, New Zealand
| | - Sai T. Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland,Botnar Research Centre for Child Health, Basel 4058, Switzerland,Corresponding author
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11
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On the Origins of Omicron's Unique Spike Gene Insertion. Vaccines (Basel) 2022; 10:vaccines10091509. [PMID: 36146586 PMCID: PMC9504260 DOI: 10.3390/vaccines10091509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 01/28/2023] Open
Abstract
The emergence of a heavily mutated SARS-CoV-2 variant (Omicron; Pango lineage B.1.1.529 and BA sublineages) and its rapid spread to over 75 countries raised a global public health alarm. Characterizing the mutational profile of Omicron is necessary to interpret its clinical phenotypes which are shared with or distinctive from those of other SARS-CoV-2 variants. We compared the mutations of the initially circulating Omicron variant (now known as BA.1) with prior variants of concern (Alpha, Beta, Gamma, and Delta), variants of interest (Lambda, Mu, Eta, Iota, and Kappa), and ~1500 SARS-CoV-2 lineages constituting ~5.8 million SARS-CoV-2 genomes. Omicron's Spike protein harbors 26 amino acid mutations (23 substitutions, 2 deletions, and 1 insertion) that are distinct compared to other variants of concern. While the substitution and deletion mutations appeared in previous SARS-CoV-2 lineages, the insertion mutation (ins214EPE) was not previously observed in any other SARS-CoV-2 lineage. Here, we consider and discuss various mechanisms through which the nucleotide sequence encoding for ins214EPE could have been acquired, including local duplication, polymerase slippage, and template switching. Although we are not able to definitively determine the mechanism, we highlight the plausibility of template switching. Analysis of the homology of the inserted nucleotide sequence and flanking regions suggests that this template-switching event could have involved the genomes of SARS-CoV-2 variants (e.g., the B.1.1 strain), other human coronaviruses that infect the same host cells as SARS-CoV-2 (e.g., HCoV-OC43 or HCoV-229E), or a human transcript expressed in a host cell that was infected by the Omicron precursor.
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12
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Wozney AJ, Smith MA, Abdrabbo M, Birch CM, Cicigoi KA, Dolan CC, Gerzema AEL, Hansen A, Henseler EJ, LaBerge B, Leavens CM, Le CN, Lindquist AC, Ludwig RK, O'Reilly MG, Reynolds JH, Sherman BA, Sillman HW, Smith MA, Snortheim MJ, Svaren LM, Vanderpas EC, Voon A, Wackett MJ, Weiss MM, Hati S, Bhattacharyya S. Evolution of Stronger SARS-CoV-2 Variants as Revealed Through the Lens of Molecular Dynamics Simulations. Protein J 2022; 41:444-456. [PMID: 35913554 PMCID: PMC9340756 DOI: 10.1007/s10930-022-10065-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2022] [Indexed: 12/03/2022]
Abstract
Using molecular dynamics simulations, the protein–protein interactions of the receptor-binding domain of the wild-type and seven variants of the severe acute respiratory syndrome coronavirus 2 spike protein and the peptidase domain of human angiotensin-converting enzyme 2 were investigated. These variants are alpha, beta, gamma, delta, eta, kappa, and omicron. Using 100 ns simulation data, the residue interaction networks at the protein–protein interface were identified. Also, the impact of mutations on essential protein dynamics, backbone flexibility, and interaction energy of the simulated protein–protein complexes were studied. The protein–protein interface for the wild-type, delta, and omicron variants contained several stronger interactions, while the alpha, beta, gamma, eta, and kappa variants exhibited an opposite scenario as evident from the analysis of the inter-residue interaction distances and pair-wise interaction energies. The study reveals that two distinct residue networks at the central and right contact regions forge stronger binding affinity between the protein partners. The study provides a molecular-level insight into how enhanced transmissibility and infectivity by delta and omicron variants are most likely tied to a handful of interacting residues at the binding interface, which could potentially be utilized for future antibody constructs and structure-based antiviral drug design.
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Affiliation(s)
- Alec J Wozney
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Macey A Smith
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Mobeen Abdrabbo
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Cole M Birch
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Kelsey A Cicigoi
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Connor C Dolan
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Audrey E L Gerzema
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Abby Hansen
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Ethan J Henseler
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Ben LaBerge
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Caterra M Leavens
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Christine N Le
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Allison C Lindquist
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Rikaela K Ludwig
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Maggie G O'Reilly
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Jacob H Reynolds
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Brandon A Sherman
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Hunter W Sillman
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Michael A Smith
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Marissa J Snortheim
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Levi M Svaren
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Emily C Vanderpas
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Aidan Voon
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Miles J Wackett
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Moriah M Weiss
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Sanchita Hati
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA.
| | - Sudeep Bhattacharyya
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA.
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13
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Williams A, Zhan CG. Fast Prediction of Binding Affinities of SARS-CoV-2 Spike Protein and Its Mutants with Antibodies through Intermolecular Interaction Modeling-Based Machine Learning. J Phys Chem B 2022; 126:5194-5206. [PMID: 35817617 PMCID: PMC9301770 DOI: 10.1021/acs.jpcb.2c02123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/28/2022] [Indexed: 11/30/2022]
Abstract
Since the introduction of the novel SARS-CoV-2 virus (COVID-19) in late 2019, various new variants have appeared with mutations that confer resistance to the vaccines and monoclonal antibodies that were developed in response to the wild-type virus. As we continue through the pandemic, an accurate and efficient methodology is needed to help predict the effects certain mutations will have on both our currently produced therapeutics and those that are in development. Using published cryo-electron microscopy and X-ray crystallography structures of the spike receptor binding domain region with currently known antibodies, in the present study, we created and cross-validated an intermolecular interaction modeling-based multi-layer perceptron machine learning approach that can accurately predict the mutation-caused shifts in the binding affinity between the spike protein (wild-type or mutant) and various antibodies. This validated artificial intelligence (AI) model was used to predict the binding affinity (Kd) of reported SARS-CoV-2 antibodies with various variants of concern, including the most recently identified "Deltamicron" (or "Deltacron") variant. This AI model may be employed in the future to predict the Kd of developed novel antibody therapeutics to overcome the challenging antibody resistance issue and develop structural bases for the effects of both current and new mutants of the spike protein. In addition, the similar AI strategy and approach based on modeling of the intermolecular interactions may be useful in development of machine learning models predicting binding affinities for other protein-protein binding systems, including other antibodies binding with their antigens.
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Affiliation(s)
- Alexander
H. Williams
- Molecular
Modeling and Biopharmaceutical Center, University
of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
| | - Chang-Guo Zhan
- Molecular
Modeling and Biopharmaceutical Center, University
of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
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14
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Eskandarzade N, Ghorbani A, Samarfard S, Diaz J, Guzzi PH, Fariborzi N, Tahmasebi A, Izadpanah K. Network for network concept offers new insights into host- SARS-CoV-2 protein interactions and potential novel targets for developing antiviral drugs. Comput Biol Med 2022; 146:105575. [PMID: 35533462 PMCID: PMC9055686 DOI: 10.1016/j.compbiomed.2022.105575] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 04/16/2022] [Accepted: 04/27/2022] [Indexed: 01/08/2023]
Abstract
SARS-CoV-2, the causal agent of COVID-19, is primarily a pulmonary virus that can directly or indirectly infect several organs. Despite many studies carried out during the current COVID-19 pandemic, some pathological features of SARS-CoV-2 have remained unclear. It has been recently attempted to address the current knowledge gaps on the viral pathogenicity and pathological mechanisms via cellular-level tropism of SARS-CoV-2 using human proteomics, visualization of virus-host protein-protein interactions (PPIs), and enrichment analysis of experimental results. The synergistic use of models and methods that rely on graph theory has enabled the visualization and analysis of the molecular context of virus/host PPIs. We review current knowledge on the SARS-COV-2/host interactome cascade involved in the viral pathogenicity through the graph theory concept and highlight the hub proteins in the intra-viral network that create a subnet with a small number of host central proteins, leading to cell disintegration and infectivity. Then we discuss the putative principle of the "gene-for-gene and "network for network" concepts as platforms for future directions toward designing efficient anti-viral therapies.
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Affiliation(s)
- Neda Eskandarzade
- Department of Basic Sciences, School of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Abozar Ghorbani
- Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, Iran,Corresponding author
| | - Samira Samarfard
- Berrimah Veterinary Laboratory, Department of Primary Industry and Resources, Berrimah, NT, 0828, Australia
| | - Jose Diaz
- Laboratorio de Dinámica de Redes Genéticas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Pietro H. Guzzi
- Department of Medical and Surgical Sciences, Laboratory of Bioinformatics Unit, Italy
| | - Niloofar Fariborzi
- Department of Medical Entomology and Vector Control, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Tahmasebi
- Institute of Biotechnology, College of Agriculture, Shiraz University, Shiraz, Iran
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15
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Sun C, Xie C, Bu GL, Zhong LY, Zeng MS. Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants. Signal Transduct Target Ther 2022; 7:202. [PMID: 35764603 PMCID: PMC9240077 DOI: 10.1038/s41392-022-01039-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/16/2022] [Accepted: 05/22/2022] [Indexed: 01/18/2023] Open
Abstract
The persistent COVID-19 pandemic since 2020 has brought an enormous public health burden to the global society and is accompanied by various evolution of the virus genome. The consistently emerging SARS-CoV-2 variants harboring critical mutations impact the molecular characteristics of viral proteins and display heterogeneous behaviors in immune evasion, transmissibility, and the clinical manifestation during infection, which differ each strain and endow them with distinguished features during populational spread. Several SARS-CoV-2 variants, identified as Variants of Concern (VOC) by the World Health Organization, challenged global efforts on COVID-19 control due to the rapid worldwide spread and enhanced immune evasion from current antibodies and vaccines. Moreover, the recent Omicron variant even exacerbated the global anxiety in the continuous pandemic. Its significant evasion from current medical treatment and disease control even highlights the necessity of combinatory investigation of the mutational pattern and influence of the mutations on viral dynamics against populational immunity, which would greatly facilitate drug and vaccine development and benefit the global public health policymaking. Hence in this review, we summarized the molecular characteristics, immune evasion, and impacts of the SARS-CoV-2 variants and focused on the parallel comparison of different variants in mutational profile, transmissibility and tropism alteration, treatment effectiveness, and clinical manifestations, in order to provide a comprehensive landscape for SARS-CoV-2 variant research.
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Affiliation(s)
- Cong Sun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Chu Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Guo-Long Bu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Lan-Yi Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China. .,Guangdong-Hong Kong Joint Laboratory for RNA Medicine, 510060, Guangzhou, China.
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16
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Bajpai P, Singh V, Chandele A, Kumar S. Broadly Neutralizing Antibodies to SARS-CoV-2 Provide Novel Insights Into the Neutralization of Variants and Other Human Coronaviruses. Front Cell Infect Microbiol 2022; 12:928279. [PMID: 35782120 PMCID: PMC9245455 DOI: 10.3389/fcimb.2022.928279] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/26/2022] [Indexed: 01/16/2023] Open
Affiliation(s)
| | | | | | - Sanjeev Kumar
- ICGEB-Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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17
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in 2020 and has led to an unprecedented global pandemic. Understanding the virology behind SARS-CoV-2 infection has provided key insights into our efforts to develop antiviral agents and control the COVID-19 pandemic. In this review, the authors focus on the genomic features of SARS-CoV-2, its intrahost and interhost evolution, viral dynamics in respiratory tract, and systemic dissemination.
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Affiliation(s)
- Yijia Li
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA,Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jonathan Z. Li
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA,Corresponding author. 65 Landsdowne Street, Room 421 Cambridge, MA 02139
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18
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Huang F, Chen L, Guo W, Zhou X, Feng K, Huang T, Cai Y. Identifying COVID-19 Severity-Related SARS-CoV-2 Mutation Using a Machine Learning Method. Life (Basel) 2022; 12:life12060806. [PMID: 35743837 PMCID: PMC9225528 DOI: 10.3390/life12060806] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/22/2022] [Accepted: 05/25/2022] [Indexed: 12/22/2022] Open
Abstract
SARS-CoV-2 shows great evolutionary capacity through a high frequency of genomic variation during transmission. Evolved SARS-CoV-2 often demonstrates resistance to previous vaccines and can cause poor clinical status in patients. Mutations in the SARS-CoV-2 genome involve mutations in structural and nonstructural proteins, and some of these proteins such as spike proteins have been shown to be directly associated with the clinical status of patients with severe COVID-19 pneumonia. In this study, we collected genome-wide mutation information of virulent strains and the severity of COVID-19 pneumonia in patients varying depending on their clinical status. Important protein mutations and untranslated region mutations were extracted using machine learning methods. First, through Boruta and four ranking algorithms (least absolute shrinkage and selection operator, light gradient boosting machine, max-relevance and min-redundancy, and Monte Carlo feature selection), mutations that were highly correlated with the clinical status of the patients were screened out and sorted in four feature lists. Some mutations such as D614G and V1176F were shown to be associated with viral infectivity. Moreover, previously unreported mutations such as A320V of nsp14 and I164ILV of nsp14 were also identified, which suggests their potential roles. We then applied the incremental feature selection method to each feature list to construct efficient classifiers, which can be directly used to distinguish the clinical status of COVID-19 patients. Meanwhile, four sets of quantitative rules were set up, which can help us to more intuitively understand the role of each mutation in differentiating the clinical status of COVID-19 patients. Identified key mutations linked to virologic properties will help better understand the mechanisms of infection and will aid in the development of antiviral treatments.
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Affiliation(s)
- Feiming Huang
- School of Life Sciences, Shanghai University, Shanghai 200444, China;
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China;
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) and Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai 200025, China;
| | - Xianchao Zhou
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai 200025, China;
| | - Kaiyan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou 510060, China;
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Correspondence: (T.H.); (Y.C.); Tel.: +86-21-54923269 (T.H.); +86-21-66136132 (Y.C.)
| | - Yudong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, China;
- Correspondence: (T.H.); (Y.C.); Tel.: +86-21-54923269 (T.H.); +86-21-66136132 (Y.C.)
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19
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Allen RA, Williams CL, Penrod Y, McCloskey C, Carpenter-Azevedo K, Huard RC, King E, Terence Dunn S. A pyrosequencing protocol for rapid identification of SARS-CoV-2 variants. J Med Virol 2022; 94:3661-3668. [PMID: 35416308 PMCID: PMC9088475 DOI: 10.1002/jmv.27770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/18/2022] [Accepted: 04/09/2022] [Indexed: 11/25/2022]
Abstract
Next‐generation sequencing (NGS) is the primary method used to monitor the distribution and emergence of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) variants around the world; however, it is costly and time‐consuming to perform and is not widely available in low‐resourced geographical regions. Pyrosequencing has the potential to augment surveillance efforts by providing information on specific targeted mutations for rapid identification of circulating and emerging variants. The current study describes the development of a reverse transcription (RT)‐PCR‐pyrosequencing assay targeting >65 spike protein gene (S) mutations of SARS‐CoV‐2, which permits differentiation of commonly reported variants currently circulating in the United States with a high degree of confidence. Variants typed using the assay included B.1.1.7 (Alpha), B.1.1.529 (Omicron), B.1.351 (Beta), B.1.375, B.1.427/429 (Epsilon), B.1.525 (Eta), B.1.526.1 (Iota), B.1.617.1 (Kappa), B.1.617.2 (Delta), B.1.621 (Mu), P1 (Gamma), and B.1.1 variants, all of which were confirmed by the NGS data. An electronic typing tool was developed to aid in the identification of variants based on mutations detected by pyrosequencing. The assay could provide an important typing tool for rapid identification of candidate patients for monoclonal antibody therapies and a method to supplement SARS‐CoV‐2 surveillance efforts by identification of circulating variants and novel emerging lineages.
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Affiliation(s)
| | - Christopher L Williams
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Yvonne Penrod
- OU Health Laboratories, Oklahoma City, Oklahoma, USA
| | | | | | - Richard C Huard
- Rhode Island Department of Health (RIDOH) Laboratories, Providence, Rhode Island, USA
| | - Ewa King
- Rhode Island Department of Health (RIDOH) Laboratories, Providence, Rhode Island, USA
| | - S Terence Dunn
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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20
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Li K, Wang AKY, Liu S, Fang S, Lu AZ, Shen J, Yang L, Hu CD, Yang K, Wan J. Advanced Functions Embedded in the Second Version of Database, Global Evaluation of SARS-CoV-2/hCoV-19 Sequences 2. Front Med (Lausanne) 2022; 9:813964. [PMID: 35479940 PMCID: PMC9037956 DOI: 10.3389/fmed.2022.813964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/07/2022] [Indexed: 11/22/2022] Open
Abstract
The Global Evaluation of SARS-CoV-2/hCoV-19 Sequences 2 (GESS v2 https://shiny.ph.iu.edu/GESS_v2/) is an updated version of GESS, which has offered a handy query platform to analyze single-nucleotide variants (SNVs) on millions of high coverages and high-quality severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) complete genomes provided by the Global Initiative on Sharing Avian Influenza Data (GISAID). Including the tools in the first version, the GESS v2 is embedded with new functions, which allow users to search SNVs, given the viral nucleotide or amino acid sequence. The GESS v2 helps users to identify SNVs or SARS-CoV-2 lineages enriched in countries of user's interest and show the migration path of a selected lineage on a world map during specific time periods chosen by the users. In addition, the GESS v2 can recognize the dynamic variations of newly emerging SNVs in each month to help users monitor SNVs, which will potentially become dominant soon. More importantly, multiple sets of analyzed results about SNVs can be downloaded directly from the GESS v2 by which users can conduct their own independent research. With these significant updates, the GESS v2 will continue to serve as a public open platform for researchers to explore SARS-CoV-2 evolutionary patterns from the perspectives of the prevalence and impact of SNVs.
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Affiliation(s)
- Kailing Li
- Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | | | - Sheng Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
- Collaborative Core for Cancer Bioinformatics (CB) shared by Indiana University Simon Comprehensive Cancer Center and Purdue University Center for Cancer Research, West Lafayette, IN, United States
| | - Shuyi Fang
- Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Alex Z. Lu
- Park Tudor School, Indianapolis, IN, United States
| | - Jikui Shen
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Lei Yang
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Chang-Deng Hu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, United States
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, United States
| | - Kai Yang
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Jun Wan
- Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
- Collaborative Core for Cancer Bioinformatics (CB) shared by Indiana University Simon Comprehensive Cancer Center and Purdue University Center for Cancer Research, West Lafayette, IN, United States
- The Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States
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21
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Pierros V, Kontopodis E, Stravopodis DJ, Tsangaris GT. Unique peptide signatures of SARS-CοV-2 virus against human proteome reveal variants’ immune escape and infectiveness. Heliyon 2022; 8:e09222. [PMID: 35399374 PMCID: PMC8979629 DOI: 10.1016/j.heliyon.2022.e09222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/19/2021] [Accepted: 03/21/2022] [Indexed: 10/29/2022] Open
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22
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Wotring JW, Fursmidt R, Ward L, Sexton JZ. Evaluating the in vitro efficacy of bovine lactoferrin products against SARS-CoV-2 variants of concern. J Dairy Sci 2022; 105:2791-2802. [PMID: 35221061 PMCID: PMC8872794 DOI: 10.3168/jds.2021-21247] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 12/07/2021] [Indexed: 12/15/2022]
Abstract
Bovine lactoferrin (bLF), a naturally occurring glycoprotein found in milk, has bioactive characteristics against many microbes, viruses, and other pathogens. Bovine lactoferrin strongly inhibits SARS-CoV-2 infection in vitro through direct entry inhibition and immunomodulatory mechanisms. This study reports on the anti-SARS-CoV-2 efficacy of commercially available bLF and common dairy ingredients in the human lung cell line H1437 using a custom high-content imaging and analysis pipeline. We also show for the first time that bLF has potent efficacy across different viral strains including the South African B.1.351, UK B.1.1.7, Brazilian P.1, and Indian Delta variants. Interestingly, we show that bLF is most potent against the B.1.1.7 variant [half-maximal inhibitory concentration (IC50) = 3.7 µg/mL], suggesting that this strain relies on entry mechanisms that are strongly inhibited by bLF. We also show that one of the major proteolysis products of bLF, lactoferricin B 17-41, has a modest anti-SARS-CoV-2 activity that could add to the clinical significance of this protein for SARS-CoV-2 treatment as lactoferricin is released by pepsin during digestion. Finally, we show that custom chewable lactoferrin tablets formulated in dextrose or sorbitol have equivalent potency to unformulated samples and provide an option for future human clinical trials. Lactoferrin's broad inhibition of SARS-CoV-2 variants in conjunction with the low cost and ease of production make this an exciting clinical candidate for treatment or prevention of SARS-CoV-2 in the future.
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Affiliation(s)
- Jesse W. Wotring
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor 48109
| | - Reid Fursmidt
- Department of Internal Medicine, Gastroenterology, Michigan Medicine at the University of Michigan, Ann Arbor 48109
| | - Loren Ward
- Glanbia Nutritionals, Twin Falls, ID 83301
| | - Jonathan Z. Sexton
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor 48109,Department of Internal Medicine, Gastroenterology, Michigan Medicine at the University of Michigan, Ann Arbor 48109,UM Center for Drug Repurposing, University of Michigan, Ann Arbor 48109,Michigan Institute for Clinical and Health Research (MICHR), University of Michigan, Ann Arbor 48109,Corresponding author
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23
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Tolerance of Human Fibroblasts to Benfo-Oxythiamine In Vitro. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19074112. [PMID: 35409800 PMCID: PMC8998213 DOI: 10.3390/ijerph19074112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/17/2022] [Accepted: 03/25/2022] [Indexed: 11/17/2022]
Abstract
OBJECTIVES To explore the potential application of B-OT in the aspiration tract. MATERIALS AND METHODS We conceived and optimized an in vitro model simulating the mouth-washing process to assess tolerance to B-OT on primary human gingival fibroblasts. Cells derived from 4 unrelated donors were flushed with medium containing drugs of various concentration for one minute twice daily for 3 days. RESULTS No effect was seen on the cells up to 1000 µM B-OT. In addition, we treated the cells with B-OT permanently in medium, corresponding to a systemic treatment. No effect was seen by 10 µM B-OT and only a slight reduction (approximately 10%) was seen by 100 µM B-OT. CONCLUSIONS Our results suggest good tolerance of oral cells for B-OT, favoring the further development of this antiviral reagent as a mouth-washing solution and nasal spray.
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24
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Moreno S, Alcázar B, Dueñas C, González del Castillo J, Olalla J, Antela A. Use of Antivirals in SARS-CoV-2 Infection. Critical Review of the Role of Remdesivir. Drug Des Devel Ther 2022; 16:827-841. [PMID: 35370401 PMCID: PMC8965332 DOI: 10.2147/dddt.s356951] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/04/2022] [Indexed: 12/15/2022] Open
Abstract
The aim of this report is to review the literature and shed light on the uncertainties surrounding the use of antiviral agents in general and remdesivir in COVID-19 patients. This review evaluated a battery of antiviral compounds and their effectiveness in the treatment of COVID-19 since the beginning of the pandemic. Remdesivir is the only antiviral approved by the EMA and FDA for the treatment of SARS-CoV-2 infection. This work extensively reviews remdesivir data generated from clinical trials and observational studies, paying attention to the most recent data, and focusing on outcomes to give readers a more comprehensive understanding of the results. This review also discusses the recommendations issued by official bodies during the pandemic in the light of the current knowledge. The use of remdesivir in the treatment of SARS-CoV-2 infection is justified because a virus is the causative agent that triggers the inflammatory responses and its consequences. More trials are needed to improve the management of this disease.
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Affiliation(s)
- Santiago Moreno
- Infectious Diseases Department, Hospital Universitario Ramón y Cajal, Universidad de Alcalá, IRYCIS, Madrid, Spain
| | - Bernardino Alcázar
- Respiratory Department, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Carlos Dueñas
- Internal Medicine Department, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | | | - Julián Olalla
- Internal Medicine Service, Hospital Costa del Sol, Marbella, Spain
| | - Antonio Antela
- Infectious Diseases Department, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
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25
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Jung C, Kmiec D, Koepke L, Zech F, Jacob T, Sparrer KMJ, Kirchhoff F. Omicron: What Makes the Latest SARS-CoV-2 Variant of Concern So Concerning? J Virol 2022; 96:e0207721. [PMID: 35225672 PMCID: PMC8941872 DOI: 10.1128/jvi.02077-21] [Citation(s) in RCA: 117] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/27/2022] [Indexed: 11/20/2022] Open
Abstract
Emerging strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19) pandemic, that show increased transmission fitness and/or immune evasion are classified as "variants of concern" (VOCs). Recently, a SARS-CoV-2 variant first identified in November 2021 in South Africa has been recognized as a fifth VOC, termed "Omicron." What makes this VOC so alarming is the high number of changes, especially in the viral Spike protein, and accumulating evidence for increased transmission efficiency and escape from neutralizing antibodies. In an amazingly short time, the Omicron VOC has outcompeted the previously dominating Delta VOC. However, it seems that the Omicron VOC is overall less pathogenic than other SARS-CoV-2 VOCs. Here, we provide an overview of the mutations in the Omicron genome and the resulting changes in viral proteins compared to other SARS-CoV-2 strains and discuss their potential functional consequences.
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Affiliation(s)
- Christoph Jung
- Institute of Electrochemistry, Ulm University, Ulm, Germany
| | - Dorota Kmiec
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Lennart Koepke
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Timo Jacob
- Institute of Electrochemistry, Ulm University, Ulm, Germany
| | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
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26
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Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons. PLoS One 2022; 17:e0261045. [PMID: 35263335 PMCID: PMC8906623 DOI: 10.1371/journal.pone.0261045] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 02/22/2022] [Indexed: 11/19/2022] Open
Abstract
As novel SARS-CoV-2 variants with different patterns of spike protein mutations have emerged, the susceptibility of these variants to neutralization by antibodies has been rapidly assessed. However, neutralization data are generated using different approaches and are scattered across different publications making it difficult for these data to be located and synthesized. The Stanford Coronavirus Resistance Database (CoV-RDB; https://covdb.stanford.edu) is designed to house comprehensively curated published data on the neutralizing susceptibility of SARS-CoV-2 variants and spike mutations to monoclonal antibodies (mAbs), convalescent plasma (CP), and vaccinee plasma (VP). As of December 31, 2021, CoV-RDB encompassed 257 publications including 91 (35%) containing 9,070 neutralizing mAb susceptibility results, 131 (51%) containing 16,773 neutralizing CP susceptibility results, and 178 (69%) containing 33,540 neutralizing VP results. The database also records which spike mutations are selected during in vitro passage of SARS-CoV-2 in the presence of mAbs and which emerge in persons receiving mAbs as treatment. The CoV-RDB interface interactively displays neutralizing susceptibility data at different levels of granularity by filtering and/or aggregating query results according to one or more experimental conditions. The CoV-RDB website provides a companion sequence analysis program that outputs information about mutations present in a submitted sequence and that also assists users in determining the appropriate mutation-detection thresholds for identifying non-consensus amino acids. The most recent data underlying the CoV-RDB can be downloaded in its entirety from a GitHub repository in a documented machine-readable format.
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27
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Dragoni F, Schiaroli E, Micheli V, Fiaschi L, Lai A, Zehender G, Rossetti B, Gismondo MR, Francisci D, Zazzi M, Vicenti I. Impact of SARS-CoV-2 omicron and delta sub-lineage AY.4.2 variant on neutralization by sera of patients treated with different licensed monoclonal antibodies. Clin Microbiol Infect 2022; 28:1037-1039. [PMID: 35304279 PMCID: PMC8923034 DOI: 10.1016/j.cmi.2022.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/04/2022] [Accepted: 03/05/2022] [Indexed: 12/29/2022]
Affiliation(s)
- Filippo Dragoni
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elisabetta Schiaroli
- Department of Medicine and Surgery, Clinic of Infectious Diseases, University of Perugia, Perugia, Italy
| | - Valeria Micheli
- Laboratory of Clinical Microbiology, Virology and Bioemergencies ASST Fatebenefratelli Sacco L. Sacco Hospital, Milan, Italy
| | - Lia Fiaschi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | - Barbara Rossetti
- Infectious Disease Department, USL SUDEST, Toscana, Misericordia Hospital, Grosseto, Italy
| | - Maria Rita Gismondo
- Laboratory of Clinical Microbiology, Virology and Bioemergencies ASST Fatebenefratelli Sacco L. Sacco Hospital, Milan, Italy
| | - Daniela Francisci
- Department of Medicine and Surgery, Clinic of Infectious Diseases, University of Perugia, Perugia, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy.
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28
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Duvignaud A, Lhomme E, Onaisi R, Sitta R, Gelley A, Chastang J, Piroth L, Binquet C, Dupouy J, Makinson A, Lefèvre B, Naccache JM, Roussillon C, Landman R, Wallet C, Karcher S, Journot V, Nguyen D, Pistone T, Bouchet S, Lafon ME, Molimard M, Thiébaut R, de Lamballerie X, Joseph JP, Richert L, Saint-Lary O, Djabarouti S, Wittkop L, Anglaret X, Malvy D. Inhaled ciclesonide for outpatient treatment of COVID-19 in adults at risk of adverse outcomes: a randomised controlled trial (COVERAGE). Clin Microbiol Infect 2022; 28:1010-1016. [PMID: 35304280 PMCID: PMC8920965 DOI: 10.1016/j.cmi.2022.02.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/08/2022] [Accepted: 02/20/2022] [Indexed: 12/23/2022]
Abstract
Objectives To assess the efficacy of inhaled ciclesonide in reducing the risk of adverse outcomes in COVID-19 outpatients at risk of developing severe illness. Methods COVERAGE is an open-label, randomized controlled trial. Outpatients with documented COVID-19, risk factors for aggravation, symptoms for ≤7 days, and absence of criteria for hospitalization are randomly allocated to either a control arm or one of several experimental arms, including inhaled ciclesonide. The primary efficacy endpoint is COVID-19 worsening (hospitalization, oxygen therapy at home, or death) by Day 14. Other endpoints are adverse events, maximal follow-up score on the WHO Ordinal Scale for Clinical Improvement, sustained alleviation of symptoms, cure, and RT-PCR and blood parameter evolution at Day 7. The trial's Safety Monitoring Board reviewed the first interim analysis of the ciclesonide arm and recommended halting it for futility. The results of this analysis are reported here. Results The analysis involved 217 participants (control 107, ciclesonide 110), including 111 women and 106 men. Their median age was 63 years (interquartile range 59–68), and 157 of 217 (72.4%) had at least one comorbidity. The median time since first symptom was 4 days (interquartile range 3–5). During the 28-day follow-up, 2 participants died (control 2/107 [1.9%], ciclesonide 0), 4 received oxygen therapy at home and were not hospitalized (control 2/107 [1.9%], ciclesonide 2/110 [1.8%]), and 24 were hospitalized (control 10/107 [9.3%], ciclesonide 14/110 [12.7%]). In intent-to-treat analysis of observed data, 26 participants reached the composite primary endpoint by Day 14, including 12 of 106 (11.3%, 95% CI: 6.0%–18.9%) in the control arm and 14 of 106 (13.2%; 95% CI: 7.4–21.2%) in the ciclesonide arm. Secondary outcomes were similar for both arms. Discussion Our findings are consistent with the European Medicines Agency's COVID-19 task force statement that there is currently insufficient evidence that inhaled corticosteroids are beneficial for patients with COVID-19.
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Affiliation(s)
- Alexandre Duvignaud
- Inserm 1219 Bordeaux Population Health, Université de Bordeaux, Bordeaux, France; Department of Infectious Diseases and Tropical Medicine, CHU Bordeaux, Bordeaux, France; IRD 271, Bordeaux, France
| | - Edouard Lhomme
- Inserm 1219 Bordeaux Population Health, Université de Bordeaux, Bordeaux, France; CIC 1401, EUCLID/F-CRIN Clinical Trials Platform, Bordeaux, France; Inria SISTM, Bordeaux, France; Department of Public Health, CHU Bordeaux, Bordeaux, France
| | - Racha Onaisi
- Department of General Practice, Bordeaux University, Bordeaux, France
| | - Rémi Sitta
- CIC 1401, EUCLID/F-CRIN Clinical Trials Platform, Bordeaux, France; Department of Public Health, CHU Bordeaux, Bordeaux, France
| | - Ambre Gelley
- CIC 1401, EUCLID/F-CRIN Clinical Trials Platform, Bordeaux, France
| | - Julie Chastang
- Département de Médecine Générale, Sorbonne Université, France; Inserm 1136 IPLESP, Sorbonne Université, Paris, France
| | - Lionel Piroth
- Département d'infectiologie, CHU de Dijon, Dijon, France; Module Épidémiologie Clinique, Université de Bourgogne, CIC Inserm 1432, Dijon, France
| | - Christine Binquet
- Module Épidémiologie Clinique, Université de Bourgogne, CIC Inserm 1432, Dijon, France
| | - Julie Dupouy
- Inserm 1295 CERPOP, Université Toulouse III Paul Sabatier, Toulouse, France; Département universitaire de médecine générale, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Alain Makinson
- Université. de Montpellier, Inserm 1175, CIC 1411, Montpellier, France; Département des Maladies Infectieuses, CHU de Montpellier, Montpellier, France
| | - Benjamin Lefèvre
- Service des Maladies Infectieuses et Tropicales, CHRU Nancy, Nancy, France; Université de Lorraine, APEMAC, Nancy, France
| | - Jean-Marc Naccache
- Service de Pneumologie-Allergologie-Oncologie Thoracique, Groupe Hospitalier Paris Saint Joseph, Paris, France
| | - Caroline Roussillon
- Clinical Research and Innovation Department, Safety and Vigilance Unit, CHU Bordeaux, Bordeaux, France
| | - Roland Landman
- Inserm 1137 IAME, Université Paris Diderot, IMEA, Paris, France; Service de Maladies Infectieuses et Tropicales, AP-HP, CHU Bichat-Claude Bernard, Paris, France
| | - Cédrick Wallet
- CIC 1401, EUCLID/F-CRIN Clinical Trials Platform, Bordeaux, France
| | - Sophie Karcher
- Inserm 1219 Bordeaux Population Health, Université de Bordeaux, Bordeaux, France
| | - Valérie Journot
- Inserm 1219 Bordeaux Population Health, Université de Bordeaux, Bordeaux, France
| | - Duc Nguyen
- Inserm 1219 Bordeaux Population Health, Université de Bordeaux, Bordeaux, France; Department of Infectious Diseases and Tropical Medicine, CHU Bordeaux, Bordeaux, France; IRD 271, Bordeaux, France
| | - Thierry Pistone
- Inserm 1219 Bordeaux Population Health, Université de Bordeaux, Bordeaux, France; Department of Infectious Diseases and Tropical Medicine, CHU Bordeaux, Bordeaux, France; IRD 271, Bordeaux, France
| | | | | | - Mathieu Molimard
- Clinical Research and Innovation Department, Safety and Vigilance Unit, CHU Bordeaux, Bordeaux, France
| | - Rodolphe Thiébaut
- Inserm 1219 Bordeaux Population Health, Université de Bordeaux, Bordeaux, France; CIC 1401, EUCLID/F-CRIN Clinical Trials Platform, Bordeaux, France; Inria SISTM, Bordeaux, France; Department of Public Health, CHU Bordeaux, Bordeaux, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents, IRD 190, Inserm 1207, Université Aix-Marseille, Marseille Cedex 05, France
| | | | - Laura Richert
- Inserm 1219 Bordeaux Population Health, Université de Bordeaux, Bordeaux, France; CIC 1401, EUCLID/F-CRIN Clinical Trials Platform, Bordeaux, France; Inria SISTM, Bordeaux, France; Department of Public Health, CHU Bordeaux, Bordeaux, France
| | - Olivier Saint-Lary
- Centre for Research in Epidemiology and Population Health, Inserm 1018, Université Paris-Saclay Villejuif, Villejuif Cedex, France; Faculty of Health Sciences Simone Veil, Department of Family Medicine, Univ. Versailles Saint-Quentin en Yvelines, Montigny Le Bretonneux, France
| | - Sarah Djabarouti
- Pharmacy, CHU Bordeaux, Bordeaux, France; Inserm 1034, Université de Bordeaux, Bordeaux, France
| | - Linda Wittkop
- Inserm 1219 Bordeaux Population Health, Université de Bordeaux, Bordeaux, France; CIC 1401, EUCLID/F-CRIN Clinical Trials Platform, Bordeaux, France; Inria SISTM, Bordeaux, France; Department of Public Health, CHU Bordeaux, Bordeaux, France
| | - Xavier Anglaret
- Inserm 1219 Bordeaux Population Health, Université de Bordeaux, Bordeaux, France; IRD 271, Bordeaux, France.
| | - Denis Malvy
- Inserm 1219 Bordeaux Population Health, Université de Bordeaux, Bordeaux, France; Department of Infectious Diseases and Tropical Medicine, CHU Bordeaux, Bordeaux, France; IRD 271, Bordeaux, France
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Zhang J, Ejikemeuwa A, Gerzanich V, Nasr M, Tang Q, Simard JM, Zhao RY. Understanding the Role of SARS-CoV-2 ORF3a in Viral Pathogenesis and COVID-19. Front Microbiol 2022; 13:854567. [PMID: 35356515 PMCID: PMC8959714 DOI: 10.3389/fmicb.2022.854567] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/09/2022] [Indexed: 12/11/2022] Open
Abstract
The ongoing SARS-CoV-2 pandemic has shocked the world due to its persistence, COVID-19-related morbidity and mortality, and the high mutability of the virus. One of the major concerns is the emergence of new viral variants that may increase viral transmission and disease severity. In addition to mutations of spike protein, mutations of viral proteins that affect virulence, such as ORF3a, also must be considered. The purpose of this article is to review the current literature on ORF3a, to summarize the molecular actions of SARS-CoV-2 ORF3a, and its role in viral pathogenesis and COVID-19. ORF3a is a polymorphic, multifunctional viral protein that is specific to SARS-CoV/SARS-CoV-2. It was acquired from β-CoV lineage and likely originated from bats through viral evolution. SARS-CoV-2 ORF3a is a viroporin that interferes with ion channel activities in host plasma and endomembranes. It is likely a virion-associated protein that exerts its effect on the viral life cycle during viral entry through endocytosis, endomembrane-associated viral transcription and replication, and viral release through exocytosis. ORF3a induces cellular innate and pro-inflammatory immune responses that can trigger a cytokine storm, especially under hypoxic conditions, by activating NLRP3 inflammasomes, HMGB1, and HIF-1α to promote the production of pro-inflammatory cytokines and chemokines. ORF3a induces cell death through apoptosis, necrosis, and pyroptosis, which leads to tissue damage that affects the severity of COVID-19. ORF3a continues to evolve along with spike and other viral proteins to adapt in the human cellular environment. How the emerging ORF3a mutations alter the function of SARS-CoV-2 ORF3a and its role in viral pathogenesis and COVID-19 is largely unknown. This review provides an in-depth analysis of ORF3a protein's structure, origin, evolution, and mutant variants, and how these characteristics affect its functional role in viral pathogenesis and COVID-19.
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Affiliation(s)
- Jiantao Zhang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, United States
- Research and Development Service, VA Maryland Health Care System, Baltimore, MD, United States
| | - Amara Ejikemeuwa
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Volodymyr Gerzanich
- Research and Development Service, VA Maryland Health Care System, Baltimore, MD, United States
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Mohamed Nasr
- Drug Development and Clinical Sciences Branch, Division of AIDS, NIAID, NIH, Bethesda, MD, United States
| | - Qiyi Tang
- Department of Microbiology, Howard University College of Medicine, Washington, DC, United States
| | - J. Marc Simard
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, United States
- Research and Development Service, VA Maryland Health Care System, Baltimore, MD, United States
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Richard Y. Zhao
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, United States
- Research and Development Service, VA Maryland Health Care System, Baltimore, MD, United States
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
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30
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Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. Nat Commun 2022; 13:742. [PMID: 35136050 PMCID: PMC8826856 DOI: 10.1038/s41467-022-28324-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/19/2022] [Indexed: 12/23/2022] Open
Abstract
The Delta and Kappa variants of SARS-CoV-2 co-emerged in India in late 2020, with the Delta variant underlying the resurgence of COVID-19, even in countries with high vaccination rates. In this study, we assess structural and biochemical aspects of viral fitness for these two variants using cryo-electron microscopy (cryo-EM), ACE2-binding and antibody neutralization analyses. Both variants demonstrate escape of antibodies targeting the N-terminal domain, an important immune hotspot for neutralizing epitopes. Compared to wild-type and Kappa lineages, Delta variant spike proteins show modest increase in ACE2 affinity, likely due to enhanced electrostatic complementarity at the RBD-ACE2 interface, which we characterize by cryo-EM. Unexpectedly, Kappa variant spike trimers form a structural head-to-head dimer-of-trimers assembly, which we demonstrate is a result of the E484Q mutation and with unknown biological implications. The combination of increased antibody escape and enhanced ACE2 binding provides an explanation, in part, for the rapid global dominance of the Delta variant. Saville, Mannar et al. provide a structural basis for enhanced antibody evasion and ACE2 binding by the Delta SARS-CoV-2 spike protein. They further identify a head-to-head dimer-of-trimers cryoEM reconstruction unique to the Kappa variant spike.
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31
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Lv Z, Cano KE, Jia L, Drag M, Huang TT, Olsen SK. Targeting SARS-CoV-2 Proteases for COVID-19 Antiviral Development. Front Chem 2022; 9:819165. [PMID: 35186898 PMCID: PMC8850931 DOI: 10.3389/fchem.2021.819165] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022] Open
Abstract
The emergence of severe acute respiratory syndrome (SARS-CoV-2) in 2019 marked the third occurrence of a highly pathogenic coronavirus in the human population since 2003. As the death toll surpasses 5 million globally and economic losses continue, designing drugs that could curtail infection and disease progression is critical. In the US, three highly effective Food and Drug Administration (FDA)-authorized vaccines are currently available, and Remdesivir is approved for the treatment of hospitalized patients. However, moderate vaccination rates and the sustained evolution of new viral variants necessitate the ongoing search for new antivirals. Several viral proteins have been prioritized as SARS-CoV-2 antiviral drug targets, among them the papain-like protease (PLpro) and the main protease (Mpro). Inhibition of these proteases would target viral replication, viral maturation, and suppression of host innate immune responses. Knowledge of inhibitors and assays for viruses were quickly adopted for SARS-CoV-2 protease research. Potential candidates have been identified to show inhibitory effects against PLpro and Mpro, both in biochemical assays and viral replication in cells. These results encourage further optimizations to improve prophylactic and therapeutic efficacy. In this review, we examine the latest developments of potential small-molecule inhibitors and peptide inhibitors for PLpro and Mpro, and how structural biology greatly facilitates this process.
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Affiliation(s)
- Zongyang Lv
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Kristin E. Cano
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Lijia Jia
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Tony T. Huang
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States
| | - Shaun K. Olsen
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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Planas D, Saunders N, Maes P, Guivel-Benhassine F, Planchais C, Buchrieser J, Bolland WH, Porrot F, Staropoli I, Lemoine F, Péré H, Veyer D, Puech J, Rodary J, Baele G, Dellicour S, Raymenants J, Gorissen S, Geenen C, Vanmechelen B, Wawina-Bokalanga T, Martí-Carreras J, Cuypers L, Sève A, Hocqueloux L, Prazuck T, Rey FA, Simon-Loriere E, Bruel T, Mouquet H, André E, Schwartz O. Considerable escape of SARS-CoV-2 Omicron to antibody neutralization. Nature 2022; 602:671-675. [PMID: 35016199 DOI: 10.1101/2021.12.14.472630] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/23/2021] [Indexed: 05/27/2023]
Abstract
The SARS-CoV-2 Omicron variant was first identified in November 2021 in Botswana and South Africa1-3. It has since spread to many countries and is expected to rapidly become dominant worldwide. The lineage is characterized by the presence of around 32 mutations in spike-located mostly in the N-terminal domain and the receptor-binding domain-that may enhance viral fitness and enable antibody evasion. Here we isolated an infectious Omicron virus in Belgium from a traveller returning from Egypt. We examined its sensitivity to nine monoclonal antibodies that have been clinically approved or are in development4, and to antibodies present in 115 serum samples from COVID-19 vaccine recipients or individuals who have recovered from COVID-19. Omicron was completely or partially resistant to neutralization by all monoclonal antibodies tested. Sera from recipients of the Pfizer or AstraZeneca vaccine, sampled five months after complete vaccination, barely inhibited Omicron. Sera from COVID-19-convalescent patients collected 6 or 12 months after symptoms displayed low or no neutralizing activity against Omicron. Administration of a booster Pfizer dose as well as vaccination of previously infected individuals generated an anti-Omicron neutralizing response, with titres 6-fold to 23-fold lower against Omicron compared with those against Delta. Thus, Omicron escapes most therapeutic monoclonal antibodies and, to a large extent, vaccine-elicited antibodies. However, Omicron is neutralized by antibodies generated by a booster vaccine dose.
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Affiliation(s)
- Delphine Planas
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, CNRS UMR3569, Paris, France
- Vaccine Research Institute, Créteil, France
| | - Nell Saunders
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, CNRS UMR3569, Paris, France
- École Doctorale BioSPC 562, Université de Paris, Paris, France
| | - Piet Maes
- Department of Microbiology, Laboratory of Clinical and Epidemiological Virology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | | | - Cyril Planchais
- Humoral Immunology Laboratory, Institut Pasteur, Université de Paris, INSERM U1222, Paris, France
| | - Julian Buchrieser
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, CNRS UMR3569, Paris, France
| | - William-Henry Bolland
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, CNRS UMR3569, Paris, France
- École Doctorale BioSPC 562, Université de Paris, Paris, France
| | - Françoise Porrot
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, CNRS UMR3569, Paris, France
| | - Isabelle Staropoli
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, CNRS UMR3569, Paris, France
| | - Frederic Lemoine
- Hub de Bioinformatique et Biostatistique, Institut Pasteur, Université de Paris, CNRS USR 3756, Paris, France
| | - Hélène Péré
- Laboratoire de Virologie, Service de Microbiologie, Hôpital Européen Georges Pompidou, Paris, France
- Functional Genomics of Solid Tumors (FunGeST), Centre de Recherche des Cordelier, INSERM, Université de Paris, Sorbonne Université, Paris, France
| | - David Veyer
- Laboratoire de Virologie, Service de Microbiologie, Hôpital Européen Georges Pompidou, Paris, France
- Functional Genomics of Solid Tumors (FunGeST), Centre de Recherche des Cordelier, INSERM, Université de Paris, Sorbonne Université, Paris, France
| | - Julien Puech
- Laboratoire de Virologie, Service de Microbiologie, Hôpital Européen Georges Pompidou, Paris, France
| | - Julien Rodary
- Laboratoire de Virologie, Service de Microbiologie, Hôpital Européen Georges Pompidou, Paris, France
| | - Guy Baele
- Department of Microbiology, Laboratory of Clinical and Epidemiological Virology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Simon Dellicour
- Department of Microbiology, Laboratory of Clinical and Epidemiological Virology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
| | - Joren Raymenants
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Sarah Gorissen
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Caspar Geenen
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Bert Vanmechelen
- Department of Microbiology, Laboratory of Clinical and Epidemiological Virology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Tony Wawina-Bokalanga
- Department of Microbiology, Laboratory of Clinical and Epidemiological Virology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Joan Martí-Carreras
- Department of Microbiology, Laboratory of Clinical and Epidemiological Virology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Lize Cuypers
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
| | - Aymeric Sève
- Service de Maladies Infectieuses, CHR d'Orléans, Orléans, France
| | | | - Thierry Prazuck
- Service de Maladies Infectieuses, CHR d'Orléans, Orléans, France
| | - Félix A Rey
- Structural Virology Unit, Institut Pasteur, Université de Paris, CNRS UMR3569, Paris, France
| | - Etienne Simon-Loriere
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université de Paris, Paris, France
| | - Timothée Bruel
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, CNRS UMR3569, Paris, France.
- Vaccine Research Institute, Créteil, France.
| | - Hugo Mouquet
- Humoral Immunology Laboratory, Institut Pasteur, Université de Paris, INSERM U1222, Paris, France.
| | - Emmanuel André
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium.
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium.
| | - Olivier Schwartz
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, CNRS UMR3569, Paris, France.
- Vaccine Research Institute, Créteil, France.
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33
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Sayan M, Arikan A, Isbilen M. Variant analysis of SARS-CoV-2 strains with phylogenetic analysis and the Coronavirus Antiviral and Resistance Database. J Comp Eff Res 2022; 11:157-167. [PMID: 35014556 PMCID: PMC8751628 DOI: 10.2217/cer-2021-0208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/12/2021] [Indexed: 01/16/2023] Open
Abstract
Aims: This study determined SARS-CoV-2 variations by phylogenetic and virtual phenotyping analyses. Materials & methods: Strains isolated from 143 COVID-19 cases in Turkey in April 2021 were assessed. Illumina NexteraXT library preparation kits were processed for next-generation ]sequencing. Phylogenetic (neighbor-joining method) and virtual phenotyping analyses (Coronavirus Antiviral and Resistance Database [CoV-RDB] by Stanford University) were used for variant analysis. Results: B.1.1.7-1/2 (n = 103, 72%), B.1.351 (n = 5, 3%) and B.1.525 (n = 1, 1%) were identified among 109 SARS-CoV-2 variations by phylogenetic analysis and B.1.1.7 (n = 95, 66%), B.1.351 (n = 5, 4%), B.1.617 (n = 4, 3%), B.1.525 (n = 2, 1.4%), B.1.526-1 (n = 1, 0.6%) and missense mutations (n = 15, 10%) were reported by CoV-RDB. The two methods were 85% compatible and B.1.1.7 (alpha) was the most frequent SARS-CoV-2 variation in Turkey in April 2021. Conclusion: The Stanford CoV-RDB analysis method appears useful for SARS-CoV-2 lineage surveillance.
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Affiliation(s)
- Murat Sayan
- Kocaeli University, Research & Education Hospital, PCR Unit, 41380, Kocaeli, Turkey
- Near East University, DESAM Research Institute, 99138, Nicosia, Northern Cyprus
| | - Ayse Arikan
- Near East University, DESAM Research Institute, 99138, Nicosia, Northern Cyprus
- Near East University, Department of Medical Microbiology & Clinical Microbiology, 99138, Nicosia, Northern Cyprus
| | - Murat Isbilen
- Acibadem Mehmet Ali Aydinlar University, Graduate School of Health Sciences, Department of Biostatistics & Bioinformatics, 34752, Istanbul, Turkey
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34
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Planas D, Saunders N, Maes P, Guivel-Benhassine F, Planchais C, Buchrieser J, Bolland WH, Porrot F, Staropoli I, Lemoine F, Péré H, Veyer D, Puech J, Rodary J, Baele G, Dellicour S, Raymenants J, Gorissen S, Geenen C, Vanmechelen B, Wawina-Bokalanga T, Martí-Carreras J, Cuypers L, Sève A, Hocqueloux L, Prazuck T, Rey F, Simon-Loriere E, Bruel T, Mouquet H, André E, Schwartz O. Considerable escape of SARS-CoV-2 Omicron to antibody neutralization. Nature 2021; 602:671-675. [PMID: 35016199 DOI: 10.1038/s41586-021-04389-z] [Citation(s) in RCA: 924] [Impact Index Per Article: 308.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/23/2021] [Indexed: 11/09/2022]
Abstract
The SARS-CoV-2 Omicron variant was first identified in November 2021 in Botswana and South Africa1-3. It has since then spread to many countries and is expected to rapidly become dominant worldwide. The lineage is characterized by the presence of about 32 mutations in the spike, located mostly in the N-terminal domain (NTD) and the receptor binding domain (RBD), which may enhance viral fitness and allow antibody evasion. Here, we isolated an infectious Omicron virus in Belgium, from a traveller returning from Egypt. We examined its sensitivity to 9 monoclonal antibodies (mAbs) clinically approved or in development4, and to antibodies present in 115 sera from COVID-19 vaccine recipients or convalescent individuals. Omicron was totally or partially resistant to neutralization by all mAbs tested. Sera from Pfizer or AstraZeneca vaccine recipients, sampled 5 months after complete vaccination, barely inhibited Omicron. Sera from COVID-19 convalescent patients collected 6 or 12 months post symptoms displayed low or no neutralizing activity against Omicron. Administration of a booster Pfizer dose as well as vaccination of previously infected individuals generated an anti-Omicron neutralizing response, with titers 6 to 23 fold lower against Omicron than against Delta. Thus, Omicron escapes most therapeutic monoclonal antibodies and to a large extent vaccine-elicited antibodies. Omicron remains however neutralized by antibodies generated by a booster vaccine dose.
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Affiliation(s)
- Delphine Planas
- Institut Pasteur, Université de Paris, CNRS UMR3569, Virus and Immunity Unit, 75015, Paris, France.,Vaccine Research Institute, 94000, Créteil, France
| | - Nell Saunders
- Institut Pasteur, Université de Paris, CNRS UMR3569, Virus and Immunity Unit, 75015, Paris, France.,Université de Paris, École doctorale BioSPC 562, 75013, Paris, France
| | - Piet Maes
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | | | - Cyril Planchais
- Institut Pasteur, Université de Paris, INSERM U1222, Humoral Immunology Laboratory, 75015, Paris, France
| | - Julian Buchrieser
- Institut Pasteur, Université de Paris, CNRS UMR3569, Virus and Immunity Unit, 75015, Paris, France
| | - William-Henry Bolland
- Institut Pasteur, Université de Paris, CNRS UMR3569, Virus and Immunity Unit, 75015, Paris, France.,Université de Paris, École doctorale BioSPC 562, 75013, Paris, France
| | - Françoise Porrot
- Institut Pasteur, Université de Paris, CNRS UMR3569, Virus and Immunity Unit, 75015, Paris, France
| | - Isabelle Staropoli
- Institut Pasteur, Université de Paris, CNRS UMR3569, Virus and Immunity Unit, 75015, Paris, France
| | - Frederic Lemoine
- Institut Pasteur, Université de Paris, CNRS USR 3756, Hub de Bioinformatique et Biostatistique, 75015, Paris, France
| | - Hélène Péré
- Hôpital Européen Georges Pompidou, Laboratoire de Virologie, Service de Microbiologie, 75015, Paris, France.,Centre de Recherche des Cordelier, INSERM, Université de Paris, Sorbonne Université, Functional Genomics of Solid Tumors (FunGeST), 75006, Paris, France
| | - David Veyer
- Hôpital Européen Georges Pompidou, Laboratoire de Virologie, Service de Microbiologie, 75015, Paris, France.,Centre de Recherche des Cordelier, INSERM, Université de Paris, Sorbonne Université, Functional Genomics of Solid Tumors (FunGeST), 75006, Paris, France
| | - Julien Puech
- Hôpital Européen Georges Pompidou, Laboratoire de Virologie, Service de Microbiologie, 75015, Paris, France
| | - Julien Rodary
- Hôpital Européen Georges Pompidou, Laboratoire de Virologie, Service de Microbiologie, 75015, Paris, France
| | - Guy Baele
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Simon Dellicour
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium.,Université Libre de Bruxelles, Spatial Epidemiology Lab (SpELL), Bruxelles, Belgium
| | - Joren Raymenants
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory Clinical Microbiology, Leuven, Belgium
| | - Sarah Gorissen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory Clinical Microbiology, Leuven, Belgium
| | - Caspar Geenen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory Clinical Microbiology, Leuven, Belgium
| | - Bert Vanmechelen
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Tony Wawina-Bokalanga
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Joan Martí-Carreras
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Lize Cuypers
- University Hospitals Leuven, Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, Leuven, Belgium
| | - Aymeric Sève
- CHR d'Orléans, service de maladies infectieuses, Orléans, France
| | | | - Thierry Prazuck
- CHR d'Orléans, service de maladies infectieuses, Orléans, France
| | - Félix Rey
- Institut Pasteur, Université de Paris, CNRS UMR3569, Structural Virology Unit, 75015, Paris, France
| | - Etienne Simon-Loriere
- Institut Pasteur, Université de Paris, CNRS UMR3569, G5 Evolutionary genomics of RNA viruses, 75015, Paris, France
| | - Timothée Bruel
- Institut Pasteur, Université de Paris, CNRS UMR3569, Virus and Immunity Unit, 75015, Paris, France. .,Vaccine Research Institute, 94000, Créteil, France.
| | - Hugo Mouquet
- Institut Pasteur, Université de Paris, INSERM U1222, Humoral Immunology Laboratory, 75015, Paris, France.
| | - Emmanuel André
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory Clinical Microbiology, Leuven, Belgium. .,University Hospitals Leuven, Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, Leuven, Belgium.
| | - Olivier Schwartz
- Institut Pasteur, Université de Paris, CNRS UMR3569, Virus and Immunity Unit, 75015, Paris, France. .,Vaccine Research Institute, 94000, Créteil, France.
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35
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Alkhatib M, Svicher V, Salpini R, Ambrosio FA, Bellocchi MC, Carioti L, Piermatteo L, Scutari R, Costa G, Artese A, Alcaro S, Shafer R, Ceccherini-Silberstein F. SARS-CoV-2 Variants and Their Relevant Mutational Profiles: Update Summer 2021. Microbiol Spectr 2021; 9:e0109621. [PMID: 34787497 PMCID: PMC8597642 DOI: 10.1128/spectrum.01096-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/21/2021] [Indexed: 12/13/2022] Open
Abstract
Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic caused by it, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been undergoing a genetic diversification leading to the emergence of new variants. Nevertheless, a clear definition of the genetic signatures underlying the circulating variants is still missing. Here, we provide a comprehensive insight into mutational profiles characterizing each SARS-CoV-2 variant, focusing on spike mutations known to modulate viral infectivity and/or antigenicity. We focused on variants and on specific relevant mutations reported by GISAID, Nextstrain, Outbreak.info, Pango, and Stanford database websites that were associated with any clinical/diagnostic impact, according to published manuscripts. Furthermore, 1,223,338 full-length high-quality SARS-CoV-2 genome sequences were retrieved from GISAID and used to accurately define the specific mutational patterns in each variant. Finally, mutations were mapped on the three-dimensional structure of the SARS-CoV-2 spike protein to assess their localization in the different spike domains. Overall, this review sheds light and assists in defining the genetic signatures characterizing the currently circulating variants and their clinical relevance. IMPORTANCE Since the emergence of SARS-CoV-2, several recurrent mutations, particularly in the spike protein, arose during human-to-human transmission or spillover events between humans and animals, generating distinct worrisome variants of concern (VOCs) or of interest (VOIs), designated as such due to their clinical and diagnostic impacts. Characterizing these variants and their related mutations is important in tracking SAR-CoV-2 evolution and understanding the efficacy of vaccines and therapeutics based on monoclonal antibodies, convalescent-phase sera, and direct antivirals. Our study provides a comprehensive survey of the mutational profiles characterizing the important SARS-CoV-2 variants, focusing on spike mutations and highlighting other protein mutations.
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Affiliation(s)
- Mohammad Alkhatib
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Valentina Svicher
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Romina Salpini
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Francesca Alessandra Ambrosio
- Dipartimento di Scienze della Salute, Campus S. Venuta, Università degli Studi “Magna Graecia” di Catanzaro, Catanzaro, Italy
| | | | - Luca Carioti
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Lorenzo Piermatteo
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Rossana Scutari
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Campus S. Venuta, Università degli Studi “Magna Graecia” di Catanzaro, Catanzaro, Italy
- Net4Science Academic Spin-Off, Campus S. Venuta, Università Magna Græcia di Catanzaro, Catanzaro, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Campus S. Venuta, Università degli Studi “Magna Graecia” di Catanzaro, Catanzaro, Italy
- Net4Science Academic Spin-Off, Campus S. Venuta, Università Magna Græcia di Catanzaro, Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Campus S. Venuta, Università degli Studi “Magna Graecia” di Catanzaro, Catanzaro, Italy
- Net4Science Academic Spin-Off, Campus S. Venuta, Università Magna Græcia di Catanzaro, Catanzaro, Italy
| | - Robert Shafer
- Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
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Lubin JH, Markosian C, Balamurugan D, Pasqualini R, Arap W, Burley SK, Khare SD. Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.12.472313. [PMID: 34931193 PMCID: PMC8687476 DOI: 10.1101/2021.12.12.472313] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
There is enormous ongoing interest in characterizing the binding properties of the SARS-CoV-2 Omicron Variant of Concern (VOC) (B.1.1.529), which continues to spread towards potential dominance worldwide. To aid these studies, based on the wealth of available structural information about several SARS-CoV-2 variants in the Protein Data Bank (PDB) and a modeling pipeline we have previously developed for tracking the ongoing global evolution of SARS-CoV-2 proteins, we provide a set of computed structural models (henceforth models) of the Omicron VOC receptor-binding domain (omRBD) bound to its corresponding receptor Angiotensin-Converting Enzyme (ACE2) and a variety of therapeutic entities, including neutralizing and therapeutic antibodies targeting previously-detected viral strains. We generated bound omRBD models using both experimentally-determined structures in the PDB as well as machine learningbased structure predictions as starting points. Examination of ACE2-bound omRBD models reveals an interdigitated multi-residue interaction network formed by omRBD-specific substituted residues (R493, S496, Y501, R498) and ACE2 residues at the interface, which was not present in the original Wuhan-Hu-1 RBD-ACE2 complex. Emergence of this interaction network suggests optimization of a key region of the binding interface, and positive cooperativity among various sites of residue substitutions in omRBD mediating ACE2 binding. Examination of neutralizing antibody complexes for Barnes Class 1 and Class 2 antibodies modeled with omRBD highlights an overall loss of interfacial interactions (with gain of new interactions in rare cases) mediated by substituted residues. Many of these substitutions have previously been found to independently dampen or even ablate antibody binding, and perhaps mediate antibody-mediated neutralization escape ( e.g ., K417N). We observe little compensation of corresponding interaction loss at interfaces when potential escape substitutions occur in combination. A few selected antibodies ( e.g ., Barnes Class 3 S309), however, feature largely unaltered or modestly affected protein-protein interfaces. While we stress that only qualitative insights can be obtained directly from our models at this time, we anticipate that they can provide starting points for more detailed and quantitative computational characterization, and, if needed, redesign of monoclonal antibodies for targeting the Omicron VOC Spike protein. In the broader context, the computational pipeline we developed provides a framework for rapidly and efficiently generating retrospective and prospective models for other novel variants of SARS-CoV-2 bound to entities of virological and therapeutic interest, in the setting of a global pandemic.
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Affiliation(s)
- Joseph H. Lubin
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
| | - Christopher Markosian
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - D. Balamurugan
- Office of Advanced Research Computing, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
| | - Renata Pasqualini
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Wadih Arap
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Hematology/Oncology, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Stephen K. Burley
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
- RCSB Protein Data Bank, San Diego Supercomputer Center and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92067
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
| | - Sagar D. Khare
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
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Mass spectrometric identification of immunogenic SARS-CoV-2 epitopes and cognate TCRs. Proc Natl Acad Sci U S A 2021; 118:2111815118. [PMID: 34725257 PMCID: PMC8609653 DOI: 10.1073/pnas.2111815118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2021] [Indexed: 12/24/2022] Open
Abstract
Durable protection against COVID-19 infection may be achieved by generating robust T cell responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and emerging SARS-CoV-2 variants; for those infected, effective treatments are urgently needed. For these strategies to be successful, accurate identification of T cell epitopes is critical. In this study, we used major histocompatibility complex immune precipitation, acid elution, and tandem mass spectrometry to define the SARS-CoV-2 immunopeptidome for membrane glycoprotein (MGP) and the nonstructural protein. Furthermore, taking advantage of a highly robust endogenous T cell workflow, we verify the immunogenicity of these MS-defined peptides by in vitro generation of MGP and NSP13 peptide-specific T cells and confirm T cell recognition of MGP or NSP13 endogenously expressing cell lines. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections elicit both humoral and cellular immune responses. For the prevention and treatment of COVID-19, the disease caused by SARS-CoV-2, it has become increasingly apparent that T cell responses are equally if not more important than humoral responses in mediating recovery and immune protection. One major challenge in developing T cell–based therapies for infectious and malignant diseases has been the identification of immunogenic epitopes that can elicit a meaningful T cell response. Traditionally, this has been achieved using sophisticated in silico methods to predict putative epitopes deduced from binding affinities. Our studies find that, in contrast to current convention, “immunodominant” SARS-CoV-2 peptides defined by such in silico methods often fail to elicit T cell responses recognizing naturally presented SARS-CoV-2 epitopes. We postulated that immunogenic epitopes for SARS-CoV-2 are best defined empirically by directly analyzing peptides eluted from the naturally processed peptide–major histocompatibility complex (MHC) and then validating immunogenicity by determining whether such peptides can elicit T cells recognizing SARS-CoV-2 antigen-expressing cells. Using a tandem mass spectrometry approach, we identified epitopes derived from not only structural but also nonstructural genes in regions highly conserved among SARS-CoV-2 strains, including recently recognized variants. Finally, there are no reported T cell receptor–engineered T cell technology that can redirect T cell specificity to recognize and kill SARS-CoV-2 target cells. We report here several SARS-CoV-2 epitopes defined by mass spectrometric analysis of MHC-eluted peptides, provide empiric evidence for their immunogenicity, and demonstrate engineered TCR-redirected killing.
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Rophina M, Pandhare K, Shamnath A, Imran M, Jolly B, Scaria V. ESC: a comprehensive resource for SARS-CoV-2 immune escape variants. Nucleic Acids Res 2021; 50:D771-D776. [PMID: 34643704 PMCID: PMC8728294 DOI: 10.1093/nar/gkab895] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/14/2021] [Accepted: 10/10/2021] [Indexed: 11/13/2022] Open
Abstract
Ever since the breakout of COVID-19 disease, ceaseless genomic research to inspect the epidemiology and evolution of the pathogen has been undertaken globally. Large scale viral genome sequencing and analysis have uncovered the functional impact of numerous genetic variants in disease pathogenesis and transmission. Emerging evidence of mutations in spike protein domains escaping antibody neutralization is reported. We have built a database with precise collation of manually curated variants in SARS-CoV-2 from literature with potential escape mechanisms from a range of neutralizing antibodies. This comprehensive repository encompasses a total of 5258 variants accounting for 2068 unique variants tested against 230 antibodies, patient convalescent plasma and vaccine breakthrough events. This resource enables the user to gain access to an extensive annotation of SARS-CoV-2 escape variants which would contribute to exploring and understanding the underlying mechanisms of immune response against the pathogen. The resource is available at http://clingen.igib.res.in/esc/.
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Affiliation(s)
- Mercy Rophina
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kavita Pandhare
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Afra Shamnath
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, India
| | - Mohamed Imran
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Bani Jolly
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Lennerstrand J, Palanisamy N. Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Viruses 2021; 13:1974. [PMID: 34696404 PMCID: PMC8538289 DOI: 10.3390/v13101974] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022] Open
Abstract
Several vaccines with varying efficacies have been developed and are currently administered globally to minimize the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Despite having an RNA-dependent RNA polymerase with a proofreading activity, new variants of SARS-CoV-2 are on the rise periodically. Some of the mutations in these variants, especially mutations on the spike protein, aid the virus in transmission, infectivity and host immune evasion. Further, these mutations also reduce the effectiveness of some of the current vaccines and monoclonal antibodies (mAbs). In the present study, using the available 984,769 SARS-CoV-2 nucleotide sequences on the NCBI database from the end of 2019 till 28 July 2021, we have estimated the global prevalence of so-called 'adaptive mutations' and 'mutations identified in the prolonged infections', in the receptor-binding domain (RBD) of the spike (S) protein. Irrespective of the geographical region, in the case of the adaptive mutations, N501Y (48.38%) was found to be the dominant mutation followed by L452R (17.52%), T478K (14.31%), E484K (4.69%), S477N (3.29%), K417T (1.64%), N439K (0.7%) and S494P (0.7%). Other mutations were found to be less prevalent (less than 0.7%). Since the last two months, there has been a massive increase of L452R and T478K mutations (delta variant) in certain areas. In the case of prolonged infections' mutations (long-term SARS-CoV-2 infections), V483A (0.009%) was found to be dominant followed by Q493R (0.009%), while other mutations were found in less than 0.007% of the studied sequences. The data obtained in this study will aid in the development of better infection control policies, thereby curbing the spread of this virus.
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Affiliation(s)
- Johan Lennerstrand
- Department of Medical Sciences, Section of Clinical Microbiology, Uppsala University, 751 85 Uppsala, Sweden;
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40
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Affiliation(s)
- Sanjeev Kumar
- ICGEB-Emory Vaccine Center Program, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center Program, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Amit Sharma
- Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- National Institute of Malaria Research, Dwarka, New Delhi, India
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41
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Next-Generation Bioinformatics Approaches and Resources for Coronavirus Vaccine Discovery and Development-A Perspective Review. Vaccines (Basel) 2021; 9:vaccines9080812. [PMID: 34451937 PMCID: PMC8402397 DOI: 10.3390/vaccines9080812] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/14/2021] [Accepted: 07/20/2021] [Indexed: 12/18/2022] Open
Abstract
COVID-19 is a contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To fight this pandemic, which has caused a massive death toll around the globe, researchers are putting efforts into developing an effective vaccine against the pathogen. As genome sequencing projects for several coronavirus strains have been completed, a detailed investigation of the functions of the proteins and their 3D structures has gained increasing attention. These high throughput data are a valuable resource for accelerating the emerging field of immuno-informatics, which is primarily aimed toward the identification of potential antigenic epitopes in viral proteins that can be targeted for the development of a vaccine construct eliciting a high immune response. Bioinformatics platforms and various computational tools and databases are also essential for the identification of promising vaccine targets making the best use of genomic resources, for further experimental validation. The present review focuses on the various stages of the vaccine development process and the vaccines available for COVID-19. Additionally, recent advances in genomic platforms and publicly available bioinformatics resources in coronavirus vaccine discovery together with related immunoinformatics databases and advances in technology are discussed.
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Planas D, Veyer D, Baidaliuk A, Staropoli I, Guivel-Benhassine F, Rajah MM, Planchais C, Porrot F, Robillard N, Puech J, Prot M, Gallais F, Gantner P, Velay A, Le Guen J, Kassis-Chikhani N, Edriss D, Belec L, Seve A, Courtellemont L, Péré H, Hocqueloux L, Fafi-Kremer S, Prazuck T, Mouquet H, Bruel T, Simon-Lorière E, Rey FA, Schwartz O. Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization. Nature 2021; 596:276-280. [PMID: 34237773 DOI: 10.1038/s41586-021-03777-9] [Citation(s) in RCA: 1388] [Impact Index Per Article: 462.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/29/2021] [Indexed: 12/27/2022]
Abstract
The SARS-CoV-2 B.1.617 lineage was identified in October 2020 in India1-5. Since then, it has become dominant in some regions of India and in the UK, and has spread to many other countries6. The lineage includes three main subtypes (B1.617.1, B.1.617.2 and B.1.617.3), which contain diverse mutations in the N-terminal domain (NTD) and the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein that may increase the immune evasion potential of these variants. B.1.617.2-also termed the Delta variant-is believed to spread faster than other variants. Here we isolated an infectious strain of the Delta variant from an individual with COVID-19 who had returned to France from India. We examined the sensitivity of this strain to monoclonal antibodies and to antibodies present in sera from individuals who had recovered from COVID-19 (hereafter referred to as convalescent individuals) or who had received a COVID-19 vaccine, and then compared this strain with other strains of SARS-CoV-2. The Delta variant was resistant to neutralization by some anti-NTD and anti-RBD monoclonal antibodies, including bamlanivimab, and these antibodies showed impaired binding to the spike protein. Sera collected from convalescent individuals up to 12 months after the onset of symptoms were fourfold less potent against the Delta variant relative to the Alpha variant (B.1.1.7). Sera from individuals who had received one dose of the Pfizer or the AstraZeneca vaccine had a barely discernible inhibitory effect on the Delta variant. Administration of two doses of the vaccine generated a neutralizing response in 95% of individuals, with titres three- to fivefold lower against the Delta variant than against the Alpha variant. Thus, the spread of the Delta variant is associated with an escape from antibodies that target non-RBD and RBD epitopes of the spike protein.
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Affiliation(s)
- Delphine Planas
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France.,Vaccine Research Institute, Creteil, France
| | - David Veyer
- INSERM, Functional Genomics of Solid Tumors (FunGeST), Centre de Recherche des Cordeliers, Université de Paris and Sorbonne Université, Paris, France.,Laboratoire de Virologie, Service de Microbiologie, Hôpital Européen Georges Pompidou, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Artem Baidaliuk
- G5 Evolutionary Genomics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
| | - Isabelle Staropoli
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France
| | | | - Maaran Michael Rajah
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Cyril Planchais
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, INSERM U1222, Paris, France
| | - Françoise Porrot
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France
| | - Nicolas Robillard
- Laboratoire de Virologie, Service de Microbiologie, Hôpital Européen Georges Pompidou, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Julien Puech
- Laboratoire de Virologie, Service de Microbiologie, Hôpital Européen Georges Pompidou, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Matthieu Prot
- G5 Evolutionary Genomics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
| | - Floriane Gallais
- CHU de Strasbourg, Laboratoire de Virologie, Strasbourg, France.,Université de Strasbourg, INSERM, IRM UMR_S 1109, Strasbourg, France
| | - Pierre Gantner
- CHU de Strasbourg, Laboratoire de Virologie, Strasbourg, France.,Université de Strasbourg, INSERM, IRM UMR_S 1109, Strasbourg, France
| | - Aurélie Velay
- CHU de Strasbourg, Laboratoire de Virologie, Strasbourg, France.,Université de Strasbourg, INSERM, IRM UMR_S 1109, Strasbourg, France
| | - Julien Le Guen
- Service de Gériatrie, Hôpital Européen Georges Pompidou, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Najiby Kassis-Chikhani
- Unité d'Hygiène Hospitalière, Service de Microbiologie, Hôpital Européen Georges Pompidou, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Dhiaeddine Edriss
- Laboratoire de Virologie, Service de Microbiologie, Hôpital Européen Georges Pompidou, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Laurent Belec
- Laboratoire de Virologie, Service de Microbiologie, Hôpital Européen Georges Pompidou, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Aymeric Seve
- CHR d'Orléans, Service de Maladies Infectieuses, Orléans, France
| | | | - Hélène Péré
- INSERM, Functional Genomics of Solid Tumors (FunGeST), Centre de Recherche des Cordeliers, Université de Paris and Sorbonne Université, Paris, France
| | | | - Samira Fafi-Kremer
- CHU de Strasbourg, Laboratoire de Virologie, Strasbourg, France.,Université de Strasbourg, INSERM, IRM UMR_S 1109, Strasbourg, France
| | - Thierry Prazuck
- CHR d'Orléans, Service de Maladies Infectieuses, Orléans, France
| | - Hugo Mouquet
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, INSERM U1222, Paris, France
| | - Timothée Bruel
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France. .,Vaccine Research Institute, Creteil, France.
| | - Etienne Simon-Lorière
- G5 Evolutionary Genomics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
| | - Felix A Rey
- Structural Virology Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France
| | - Olivier Schwartz
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France. .,Vaccine Research Institute, Creteil, France.
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Hill A, Garratt A, Levi J, Falconer J, Ellis L, McCann K, Pilkington V, Qavi A, Wang J, Wentzel H. Meta-analysis of randomized trials of ivermectin to treat SARS-CoV-2 infection. Open Forum Infect Dis 2021; 8:ofab358. [PMID: 34796244 PMCID: PMC8420640 DOI: 10.1093/ofid/ofab358] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 07/05/2021] [Indexed: 12/15/2022] Open
Abstract
Ivermectin is an antiparasitic drug being investigated for repurposing against severe
acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Ivermectin showed in vitro activity
against SARS-COV-2, but only at high concentrations. This meta-analysis investigated
ivermectin in 23 randomized clinical trials (3349 patients) identified through systematic
searches of PUBMED, EMBASE, MedRxiv, and trial registries. The primary meta-analysis was
carried out by excluding studies at a high risk of bias. Ivermectin did not show a
statistically significant effect on survival (risk ratio [RR], 0.90; 95% CI, 0.57 to 1.42;
P = .66) or hospitalizations (RR, 0.63; 95% CI, 0.36 to 1.11;
P = .11). Ivermectin displayed a borderline significant effect on
duration of hospitalization in comparison with standard of care (mean difference, –1.14
days; 95% CI, –2.27 to –0.00; P = .05). There was no significant effect
of ivermectin on time to clinical recovery (mean difference, –0.57 days; 95% CI, –1.31 to
0.17; P = .13) or binary clinical recovery (RR, 1.19; 95% CI, 0.94 to
1.50; P = .15). Currently, the World Health Organization recommends the
use of ivermectin only inside clinical trials. A network of large clinical trials is in
progress to validate the results seen to date.
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Affiliation(s)
- Andrew Hill
- Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, L7 3NY, UK
| | - Anna Garratt
- Department of Infectious Diseases, University Hospital of Wales, Cardiff and Vale University Health Board, UK
| | - Jacob Levi
- Department of Intensive Care, University College London Hospital, ULCH NHS Trust, London, UK
| | - Jonathan Falconer
- Department of Infectious Diseases, Chelsea and Westminster Hospital, Imperial NHS Trust, London, UK
| | - Leah Ellis
- Faculty of Medicine, Imperial College London, UK
| | | | - Victoria Pilkington
- Oxford University Clinical Academic Graduate School, University of Oxford, UK
| | - Ambar Qavi
- Faculty of Medicine, Imperial College London, UK
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Serafim MSM, Dos Santos Júnior VS, Gertrudes JC, Maltarollo VG, Honorio KM. Machine learning techniques applied to the drug design and discovery of new antivirals: a brief look over the past decade. Expert Opin Drug Discov 2021; 16:961-975. [PMID: 33957833 DOI: 10.1080/17460441.2021.1918098] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Introduction: Drug design and discovery of new antivirals will always be extremely important in medicinal chemistry, taking into account known and new viral diseases that are yet to come. Although machine learning (ML) have shown to improve predictions on the biological potential of chemicals and accelerate the discovery of drugs over the past decade, new methods and their combinations have improved their performance and established promising perspectives regarding ML in the search for new antivirals.Areas covered: The authors consider some interesting areas that deal with different ML techniques applied to antivirals. Recent innovative studies on ML and antivirals were selected and analyzed in detail. Also, the authors provide a brief look at the past to the present to detect advances and bottlenecks in the area.Expert opinion: From classical ML techniques, it was possible to boost the searches for antivirals. However, from the emergence of new algorithms and the improvement in old approaches, promising results will be achieved every day, as we have observed in the case of SARS-CoV-2. Recent experience has shown that it is possible to use ML to discover new antiviral candidates from virtual screening and drug repurposing.
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Affiliation(s)
- Mateus Sá Magalhães Serafim
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | | | - Jadson Castro Gertrudes
- Departamento de Computação, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto (UFOP), Ouro Preto, Brazil
| | - Vinícius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Kathia Maria Honorio
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo (USP), São Paulo, Brazil.,Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, Brazil
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Vicenti I, Zazzi M, Saladini F. SARS-CoV-2 RNA-dependent RNA polymerase as a therapeutic target for COVID-19. Expert Opin Ther Pat 2021; 31:325-337. [PMID: 33475441 PMCID: PMC7938656 DOI: 10.1080/13543776.2021.1880568] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/20/2021] [Indexed: 02/08/2023]
Abstract
Introduction: The current SARS-CoV-2 pandemic urgently demands for both prevention and treatment strategies. RNA-dependent RNA-polymerase (RdRp), which has no counterpart in human cells, is an excellent target for drug development. Given the time-consuming process of drug development, repurposing drugs approved for other indications or at least successfully tested in terms of safety and tolerability, is an attractive strategy to rapidly provide an effective medication for severe COVID-19 cases.Areas covered: The currently available data and upcominSg studies on RdRp which can be repurposed to halt SARS-CoV-2 replication, are reviewed.Expert opinion: Drug repurposing and design of novel compounds are proceeding in parallel to provide a quick response and new specific drugs, respectively. Notably, the proofreading SARS-CoV-2 exonuclease activity could limit the potential for drugs designed as immediate chain terminators and favor the development of compounds acting through delayed termination. While vaccination is awaited to curb the SARS-CoV-2 epidemic, even partially effective drugs from repurposing strategies can be of help to treat severe cases of disease. Considering the high conservation of RdRp among coronaviruses, an improved knowledge of its activity in vitro can provide useful information for drug development or drug repurposing to combat SARS-CoV-2 as well as future pandemics.
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Affiliation(s)
- Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
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Shafer RW. A SARS-CoV-2 antiviral therapy score card. Glob Health Med 2020; 2:346-349. [PMID: 33409413 PMCID: PMC7780285 DOI: 10.35772/ghm.2020.01082] [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: 09/01/2020] [Revised: 09/07/2020] [Accepted: 09/13/2020] [Indexed: 06/12/2023]
Abstract
The COVID-19 pandemic has unleashed an unprecedented effort to identify efficacious treatments for persons infected with SARS-CoV-2. As of September 2020, more than 750 completed, ongoing, or planned clinical trials of drugs intended to inhibit SARS-CoV-2 replication have been registered on the ClinicalTrials.gov or WHO International Clinical Trials Platform websites. Most of the treatments studied in these trials are repurposed licensed or investigational drugs targeting viral proteins or cellular pathways required for virus replication. The use of repurposed compounds is understandable because with the exception of monoclonal antibodies, it will be several months before novel SARS-CoV-2-specific drugs will be available for human testing. This editorial describes those compounds that I believe should be prioritized for clinical testing: i) viral RNA polymerase inhibitors including GS-441524, its prodrug remdesivir, and EIDD-2801; ii) entry inhibitors including monoclonal antibodies, ACE2 molecular decoys, and peptide fusion inhibitors; iii) parenteral and inhalational preparations of interferon β and λ; and iv) inhibitors of host transmembrane protease serine 2 (TMPRSS2), endosomal trafficking, and pyrimidine synthesis. As SARS-CoV-2 is pandemic and as its most severe consequences result from a dysregulated immunological response to infection, the ideal therapies should be inexpensive and should be able to be administered to non-hospitalized persons at the time of their initial diagnosis.
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Affiliation(s)
- Robert W. Shafer
- Address correspondence to:Robert W. Shafer, Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, 1000 Welch Rd Ste 202, Palo Alto, CA 94304, USA. E-mail:
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