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Casadevall A, Focosi D. SARS-CoV-2 variants resistant to monoclonal antibodies in immunocompromised patients constitute a public health concern. J Clin Invest 2023; 133:e168603. [PMID: 36919696 PMCID: PMC10014096 DOI: 10.1172/jci168603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
COVID-19 in immunocompromised hosts has emerged as a difficult therapeutic management problem. Immunocompromised hosts mount weak responses to SARS-CoV-2 and manifest infection outcomes ranging from severe disease to persistent infection. Weakened immune systems mean greater viral loads and increased opportunities for viral evolution. Gupta, Konnova, et al. report the emergence of resistant SARS-CoV-2 variants in immunocompromised patients after monoclonal antibody (mAb) therapy. mAbs target only a single determinant in the viral Spike protein, which is a weakness of such therapy when treating a mutagenic and variable virus. Hence, the emergence of mAb resistance could have been anticipated, but its documentation is important because it has major public health implications, since such resistant variants have the potential to spread and escape vaccine immunity. For immunocompromised patients, these findings suggest the need for combination therapy with antiviral drugs and the use of polyclonal antibody preparations such as convalescent plasma.
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Affiliation(s)
- Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
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2
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Marano JM, Weger-Lucarelli J. Replication in the presence of dengue convalescent serum impacts Zika virus neutralization sensitivity and fitness. Front Cell Infect Microbiol 2023; 13:1130749. [PMID: 36968111 PMCID: PMC10034770 DOI: 10.3389/fcimb.2023.1130749] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/13/2023] [Indexed: 03/11/2023] Open
Abstract
IntroductionFlaviviruses like dengue virus (DENV) and Zika virus (ZIKV) are mosquito-borne viruses that cause febrile, hemorrhagic, and neurological diseases in humans, resulting in 400 million infections annually. Due to their co-circulation in many parts of the world, flaviviruses must replicate in the presence of pre-existing adaptive immune responses targeted at serologically closely related pathogens, which can provide protection or enhance disease. However, the impact of pre-existing cross-reactive immunity as a driver of flavivirus evolution, and subsequently the implications on the emergence of immune escape variants, is poorly understood. Therefore, we investigated how replication in the presence of convalescent dengue serum drives ZIKV evolution.MethodsWe used an in vitro directed evolution system, passaging ZIKV in the presence of serum from humans previously infected with DENV (anti-DENV) or serum from DENV-naïve patients (control serum). Following five passages in the presence of serum, we performed next-generation sequencing to identify mutations that arose during passaging. We studied two non-synonymous mutations found in the anti-DENV passaged population (E-V355I and NS1-T139A) by generating individual ZIKV mutants and assessing fitness in mammalian cells and live mosquitoes, as well as their sensitivity to antibody neutralization.Results and discussionBoth viruses had increased fitness in Vero cells with and without the addition of anti-DENV serum and in human lung epithelial and monocyte cells. In Aedes aegypti mosquitoes—using blood meals with and without anti-DENV serum—the mutant viruses had significantly reduced fitness compared to wild-type ZIKV. These results align with the trade-off hypothesis of constrained mosquito-borne virus evolution. Notably, only the NS1-T139A mutation escaped neutralization, while E-V335I demonstrated enhanced neutralization sensitivity to neutralization by anti-DENV serum, indicating that neutralization escape is not necessary for viruses passaged under cross-reactive immune pressures. Future studies are needed to assess cross-reactive immune selection in humans and relevant animal models or with different flaviviruses.
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Affiliation(s)
- Jeffrey M. Marano
- Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Roanoke, VA, United States
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, United States
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, United States
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States
- *Correspondence: James Weger-Lucarelli,
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3
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Dang S, Ren L, Wang J. Functional mutations of SARS-CoV-2: implications to viral transmission, pathogenicity and immune escape. Chin Med J (Engl) 2022; 135:1213-1222. [PMID: 35788093 PMCID: PMC9337262 DOI: 10.1097/cm9.0000000000002158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Indexed: 11/27/2022] Open
Abstract
ABSTRACT The pandemic of coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to major public health challenges globally. The increasing viral lineages identified indicate that the SARS-CoV-2 genome is evolving at a rapid rate. Viral genomic mutations may cause antigenic drift or shift, which are important ways by which SARS-CoV-2 escapes the human immune system and changes its transmissibility and virulence. Herein, we summarize the functional mutations in SARS-CoV-2 genomes to characterize its adaptive evolution to inform the development of vaccination, treatment as well as control and intervention measures.
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Affiliation(s)
- Shengyuan Dang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Lili Ren
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jianwei Wang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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4
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Goławski M, Lewandowski P, Jabłońska I, Delijewski M. The Reassessed Potential of SARS-CoV-2 Attenuation for COVID-19 Vaccine Development—A Systematic Review. Viruses 2022; 14:v14050991. [PMID: 35632736 PMCID: PMC9146402 DOI: 10.3390/v14050991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022] Open
Abstract
Live-attenuated SARS-CoV-2 vaccines received relatively little attention during the COVID-19 pandemic. Despite this, several methods of obtaining attenuated coronaviruses are known. In this systematic review, the strategies of coronavirus attenuation, which may potentially be applied to SARS-CoV-2, were identified. PubMed, Scopus, Web of Science and Embase databases were searched to identify relevant articles describing attenuating mutations tested in vivo. In case of coronaviruses other than SARS-CoV-2, sequence alignment was used to exclude attenuating mutations that cannot be applied to SARS-CoV-2. Potential immunogenicity, safety and efficacy of the attenuated SARS-CoV-2 vaccine were discussed based on animal studies data. A total of 27 attenuation strategies, used to create 101 different coronaviruses, have been described in 56 eligible articles. The disruption of the furin cleavage site in the SARS-CoV-2 spike protein was identified as the most promising strategy. The replacement of core sequences of transcriptional regulatory signals, which prevents recombination with wild-type viruses, also appears particularly advantageous. Other important attenuating mutations encompassed mostly the prevention of evasion of innate immunity. Sufficiently attenuated coronaviruses typically caused no meaningful disease in susceptible animals and protected them from challenges with virulent virus. This indicates that attenuated COVID-19 vaccines may be considered as a potential strategy to fight the threat posed by SARS-CoV-2.
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Affiliation(s)
- Marcin Goławski
- Department of Pharmacology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland; (P.L.); (M.D.)
- Correspondence:
| | - Piotr Lewandowski
- Department of Pharmacology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland; (P.L.); (M.D.)
| | - Iwona Jabłońska
- Department of Biophysics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland;
| | - Marcin Delijewski
- Department of Pharmacology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland; (P.L.); (M.D.)
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5
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Akram F, Haq IU, Aqeel A, Ahmed Z, Shah FI, Nawaz A, Zafar J, Sattar R. Insights into the evolutionary and prophylactic analysis of SARS-CoV-2: A review. J Virol Methods 2022; 300:114375. [PMID: 34838536 PMCID: PMC8610842 DOI: 10.1016/j.jviromet.2021.114375] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 10/29/2021] [Accepted: 11/22/2021] [Indexed: 01/04/2023]
Abstract
In late 2019, following the emergence of a β-originated SARS-CoV-2, phylogenetic and evolutionary approaches have been demonstrated to strengthen the diagnostic and prophylactic stratagem of COVID-19 at an unprecedented level. Despite its clinical prominence, the SARS-CoV-2 gene set remains largely irrefutable by impeding the dissection of COVID-19 biology. However, many pieces of molecular and serological evidence have predicted that SARS-CoV-2 related viruses carry their roots from bats and pangolins of South East Asia. Analysis of viral genome predicts that point mutations at a rate of 10-4 nucleotides per base in the receptor-binding domain allow the emergence of new SARS-CoV-2 genomic variants at regular intervals. Research in the evolution of molecular pathways involved in emergence of pandemic is critical for the development of therapeutics and vaccines as well as the prevention of future zoonosis. By determining the phyletic lineages of the SARS-CoV-2 genomic variants and those of the conserved regions in the accessory and spike proteins of all the SARS-related coronaviruses, a universal vaccine against all human coronaviruses could be formulated which would revolutionize the field of medicine. This review highlighted the current development and future prospects of antiviral drugs, inhibitors, mesenchymal stem cells, passive immunization, targeted immune therapy and CRISPR-Cas-based prophylactic and therapeutic strategies against SARS-CoV-2. However, further investigations on Covid-19 pathogenesis is required for the successful fabrication of successful antivirals.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan.
| | - Ikram Ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Amna Aqeel
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Zeeshan Ahmed
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Fatima Iftikhar Shah
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Ali Nawaz
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Javaria Zafar
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Rukhma Sattar
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
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6
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Rando HM, Wellhausen N, Ghosh S, Lee AJ, Dattoli AA, Hu F, Byrd JB, Rafizadeh DN, Lordan R, Qi Y, Sun Y, Brueffer C, Field JM, Ben Guebila M, Jadavji NM, Skelly AN, Ramsundar B, Wang J, Goel RR, Park Y, Boca SM, Gitter A, Greene CS. Identification and Development of Therapeutics for COVID-19. mSystems 2021; 6:e0023321. [PMID: 34726496 PMCID: PMC8562484 DOI: 10.1128/msystems.00233-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
After emerging in China in late 2019, the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread worldwide, and as of mid-2021, it remains a significant threat globally. Only a few coronaviruses are known to infect humans, and only two cause infections similar in severity to SARS-CoV-2: Severe acute respiratory syndrome-related coronavirus, a species closely related to SARS-CoV-2 that emerged in 2002, and Middle East respiratory syndrome-related coronavirus, which emerged in 2012. Unlike the current pandemic, previous epidemics were controlled rapidly through public health measures, but the body of research investigating severe acute respiratory syndrome and Middle East respiratory syndrome has proven valuable for identifying approaches to treating and preventing novel coronavirus disease 2019 (COVID-19). Building on this research, the medical and scientific communities have responded rapidly to the COVID-19 crisis and identified many candidate therapeutics. The approaches used to identify candidates fall into four main categories: adaptation of clinical approaches to diseases with related pathologies, adaptation based on virological properties, adaptation based on host response, and data-driven identification (ID) of candidates based on physical properties or on pharmacological compendia. To date, a small number of therapeutics have already been authorized by regulatory agencies such as the Food and Drug Administration (FDA), while most remain under investigation. The scale of the COVID-19 crisis offers a rare opportunity to collect data on the effects of candidate therapeutics. This information provides insight not only into the management of coronavirus diseases but also into the relative success of different approaches to identifying candidate therapeutics against an emerging disease. IMPORTANCE The COVID-19 pandemic is a rapidly evolving crisis. With the worldwide scientific community shifting focus onto the SARS-CoV-2 virus and COVID-19, a large number of possible pharmaceutical approaches for treatment and prevention have been proposed. What was known about each of these potential interventions evolved rapidly throughout 2020 and 2021. This fast-paced area of research provides important insight into how the ongoing pandemic can be managed and also demonstrates the power of interdisciplinary collaboration to rapidly understand a virus and match its characteristics with existing or novel pharmaceuticals. As illustrated by the continued threat of viral epidemics during the current millennium, a rapid and strategic response to emerging viral threats can save lives. In this review, we explore how different modes of identifying candidate therapeutics have borne out during COVID-19.
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Affiliation(s)
- Halie M. Rando
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Center for Health AI, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Nils Wellhausen
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Soumita Ghosh
- Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Alexandra J. Lee
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anna Ada Dattoli
- Department of Systems Pharmacology & Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Fengling Hu
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - James Brian Byrd
- University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Diane N. Rafizadeh
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronan Lordan
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yanjun Qi
- Department of Computer Science, University of Virginia, Charlottesville, Virginia, USA
| | - Yuchen Sun
- Department of Computer Science, University of Virginia, Charlottesville, Virginia, USA
| | | | - Jeffrey M. Field
- Department of Systems Pharmacology & Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marouen Ben Guebila
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Nafisa M. Jadavji
- Biomedical Science, Midwestern University, Glendale, Arizona, USA
- Department of Neuroscience, Carleton University, Ottawa, Ontario, Canada
| | - Ashwin N. Skelly
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | | | - Jinhui Wang
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rishi Raj Goel
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - YoSon Park
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - COVID-19 Review Consortium
BansalVikasBartonJohn P.BocaSimina M.BoerckelJoel D.BruefferChristianByrdJames BrianCaponeStephenDasShiktaDattoliAnna AdaDziakJohn J.FieldJeffrey M.GhoshSoumitaGitterAnthonyGoelRishi RajGreeneCasey S.GuebilaMarouen BenHimmelsteinDaniel S.HuFenglingJadavjiNafisa M.KamilJeremy P.KnyazevSergeyKollaLikhithaLeeAlexandra J.LordanRonanLubianaTiagoLukanTemitayoMacLeanAdam L.MaiDavidMangulSergheiManheimDavidMcGowanLucy D’AgostinoNaikAmrutaParkYoSonPerrinDimitriQiYanjunRafizadehDiane N.RamsundarBharathRandoHalie M.RaySandipanRobsonMichael P.RubinettiVincentSellElizabethShinholsterLamonicaSkellyAshwin N.SunYuchenSunYushaSzetoGregory L.VelazquezRyanWangJinhuiWellhausenNils
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Center for Health AI, University of Colorado School of Medicine, Aurora, Colorado, USA
- Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Systems Pharmacology & Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- University of Michigan School of Medicine, Ann Arbor, Michigan, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Computer Science, University of Virginia, Charlottesville, Virginia, USA
- Department of Clinical Sciences, Lund University, Lund, Sweden
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA
- Biomedical Science, Midwestern University, Glendale, Arizona, USA
- Department of Neuroscience, Carleton University, Ottawa, Ontario, Canada
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- The DeepChem Project
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
- Early Biometrics & Statistical Innovation, Data Science & Artificial Intelligence, R & D, AstraZeneca, Gaithersburg, Maryland, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Philadelphia, Pennsylvania, USA
| | - Simina M. Boca
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
- Early Biometrics & Statistical Innovation, Data Science & Artificial Intelligence, R & D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Anthony Gitter
- Department of Biostatistics and Medical Informatics, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Casey S. Greene
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Center for Health AI, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Systems Pharmacology & Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Philadelphia, Pennsylvania, USA
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7
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Focosi D, Maggi F. Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. Rev Med Virol 2021; 31:e2231. [PMID: 33724631 PMCID: PMC8250244 DOI: 10.1002/rmv.2231] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/29/2021] [Accepted: 02/15/2021] [Indexed: 12/15/2022]
Abstract
The Spike protein is the target of both antibody-based therapeutics (convalescent plasma, polyclonal serum, monoclonal antibodies) and vaccines. Mutations in Spike could affect efficacy of those treatments. Hence, monitoring of mutations is necessary to forecast and readapt the inventory of therapeutics. Different phylogenetic nomenclatures have been used for the currently circulating SARS-CoV-2 clades. The Spike protein has different hotspots of mutation and deletion, the most dangerous for immune escape being the ones within the receptor binding domain (RBD), such as K417N/T, N439K, L452R, Y453F, S477N, E484K, and N501Y. Convergent evolution has led to different combinations of mutations among different clades. In this review we focus on the main variants of concern, that is, the so-called UK (B.1.1.7), South African (B.1.351) and Brazilian (P.1) strains.
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MESH Headings
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/metabolism
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/metabolism
- Antibodies, Neutralizing/therapeutic use
- Antibodies, Viral/chemistry
- Antibodies, Viral/metabolism
- Antibodies, Viral/therapeutic use
- Brazil/epidemiology
- COVID-19/epidemiology
- COVID-19/immunology
- COVID-19/therapy
- COVID-19/virology
- COVID-19 Vaccines/administration & dosage
- Gene Expression
- Humans
- Immune Evasion
- Immunization, Passive/methods
- Mutation
- Phylogeny
- Protein Binding
- Risk Assessment
- SARS-CoV-2/classification
- SARS-CoV-2/drug effects
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- South Africa/epidemiology
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- United Kingdom/epidemiology
- COVID-19 Serotherapy
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Affiliation(s)
- Daniele Focosi
- North‐Western Tuscany Blood BankPisa University HospitalPisaItaly
| | - Fabrizio Maggi
- Department of Medicine and SurgeryUniversity of InsubriaVareseItaly
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8
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Esmaeilzadeh A, Rostami S, Yeganeh PM, Tahmasebi S, Ahmadi M. Recent advances in antibody-based immunotherapy strategies for COVID-19. J Cell Biochem 2021; 122:1389-1412. [PMID: 34160093 PMCID: PMC8427040 DOI: 10.1002/jcb.30017] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 01/09/2023]
Abstract
The emergence of a new acute respiratory syndrome Coronavirus 2 (SARS-CoV-2), the cause of the 2019-nCOV disease (COVID-19), has caused a pandemic and a global health crisis. Rapid human-to-human transmission, even from asymptomatic individuals, has led to the quick spread of the virus worldwide, causing a wide range of clinical manifestations from cold-like symptoms to severe pneumonia, acute respiratory distress syndrome (ARDS), multiorgan injury, and even death. Therefore, using rapid and accurate diagnostic methods to identify the virus and subsequently select appropriate and effective treatments can help improvement of patients and control the pandemic. So far, various treatment regimens along with prophylactic vaccines have been developed to manage COVID-19-infected patients. Among these, antibody-based therapies, including neutralizing antibodies (against different parts of the virus), polyclonal and monoclonal antibodies, plasma therapy, and high-dose intravenous immunoglobulin (IVIG) have shown promising outcomes in accelerating and improving the treatment process of patients, avoiding the viral spreading widely, and managing the pandemic. In the current review paper, different types and applications of therapeutic antibodies in the COVID-19 treatment are comprehensively discussed.
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Affiliation(s)
- Abdolreza Esmaeilzadeh
- Department of Immunology, School of MedicineZanjan University of Medical SciencesZanjanIran
- Immunotherapy Research and Technology GroupZanjan University of Medical SciencesZanjanIran
| | - Samaneh Rostami
- Department of immunology, School of medicineZanjan University of Medical SciencesZanjanIran
| | - Pegah M. Yeganeh
- Department of immunology, School of medicineZanjan University of Medical SciencesZanjanIran
| | - Safa Tahmasebi
- Department of Immunology, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Majid Ahmadi
- Stem Cell Research CenterTabriz University of Medical SciencesTabrizIran
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9
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Liu X, Luo Y, Li P, Song S, Peng J. Deep geometric representations for modeling effects of mutations on protein-protein binding affinity. PLoS Comput Biol 2021; 17:e1009284. [PMID: 34347784 PMCID: PMC8366979 DOI: 10.1371/journal.pcbi.1009284] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 08/16/2021] [Accepted: 07/17/2021] [Indexed: 11/19/2022] Open
Abstract
Modeling the impact of amino acid mutations on protein-protein interaction plays a crucial role in protein engineering and drug design. In this study, we develop GeoPPI, a novel structure-based deep-learning framework to predict the change of binding affinity upon mutations. Based on the three-dimensional structure of a protein, GeoPPI first learns a geometric representation that encodes topology features of the protein structure via a self-supervised learning scheme. These representations are then used as features for training gradient-boosting trees to predict the changes of protein-protein binding affinity upon mutations. We find that GeoPPI is able to learn meaningful features that characterize interactions between atoms in protein structures. In addition, through extensive experiments, we show that GeoPPI achieves new state-of-the-art performance in predicting the binding affinity changes upon both single- and multi-point mutations on six benchmark datasets. Moreover, we show that GeoPPI can accurately estimate the difference of binding affinities between a few recently identified SARS-CoV-2 antibodies and the receptor-binding domain (RBD) of the S protein. These results demonstrate the potential of GeoPPI as a powerful and useful computational tool in protein design and engineering. Our code and datasets are available at: https://github.com/Liuxg16/GeoPPI. Estimating the binding affinities of protein-protein interactions (PPIs) is crucial to understand protein function and design new functional proteins. Since the experimental measurement in wet-labs is labor-intensive and time-consuming, fast and accurate in silico approaches have received much attention. Although considerable efforts have been made in this direction, predicting the effects of mutations on the protein-protein binding affinity is still a challenging research problem. In this work, we introduce GeoPPI, a novel computational approach that uses deep geometric representations of protein complexes to predict the effects of mutations on the binding affinity. The geometric representations are first learned via a self-supervised learning scheme and then integrated with gradient-boosting trees to accomplish the prediction. We find that the learned representations encode meaningful patterns underlying the interactions between atoms in protein structures. Also, extensive tests on major benchmark datasets show that GeoPPI has made an important improvement over the existing methods in predicting the effects of mutations on the binding affinity.
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Affiliation(s)
- Xianggen Liu
- Laboratory for Brain and Intelligence and Department of Biomedical Engineering, Tsinghua University, Beijing, China
- School of Computing and Artificial Intelligence, Southwest Jiaotong University, Chengdu, China
- Beijing Innovation Center for Future Chip, Tsinghua University, Beijing, China
| | - Yunan Luo
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Pengyong Li
- Laboratory for Brain and Intelligence and Department of Biomedical Engineering, Tsinghua University, Beijing, China
- Beijing Innovation Center for Future Chip, Tsinghua University, Beijing, China
| | - Sen Song
- Laboratory for Brain and Intelligence and Department of Biomedical Engineering, Tsinghua University, Beijing, China
- Beijing Innovation Center for Future Chip, Tsinghua University, Beijing, China
- * E-mail: (JP); (SS)
| | - Jian Peng
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail: (JP); (SS)
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10
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Structural basis for broad coronavirus neutralization. Nat Struct Mol Biol 2021; 28:478-486. [PMID: 33981021 DOI: 10.1038/s41594-021-00596-4] [Citation(s) in RCA: 133] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/21/2021] [Indexed: 02/03/2023]
Abstract
Three highly pathogenic β-coronaviruses have crossed the animal-to-human species barrier in the past two decades: SARS-CoV, MERS-CoV and SARS-CoV-2. To evaluate the possibility of identifying antibodies with broad neutralizing activity, we isolated a monoclonal antibody, termed B6, that cross-reacts with eight β-coronavirus spike glycoproteins, including all five human-infecting β-coronaviruses. B6 broadly neutralizes entry of pseudotyped viruses from lineages A and C, but not from lineage B, and the latter includes SARS-CoV and SARS-CoV-2. Cryo-EM, X-ray crystallography and membrane fusion assays reveal that B6 binds to a conserved cryptic epitope located in the fusion machinery. The data indicate that antibody binding sterically interferes with the spike conformational changes leading to membrane fusion. Our data provide a structural framework explaining B6 cross-reactivity with β-coronaviruses from three lineages, along with a proof of concept for antibody-mediated broad coronavirus neutralization elicited through vaccination. This study unveils an unexpected target for next-generation structure-guided design of a pan-β-coronavirus vaccine.
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11
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Rees-Spear C, Muir L, Griffith SA, Heaney J, Aldon Y, Snitselaar JL, Thomas P, Graham C, Seow J, Lee N, Rosa A, Roustan C, Houlihan CF, Sanders RW, Gupta RK, Cherepanov P, Stauss HJ, Nastouli E, Doores KJ, van Gils MJ, McCoy LE. The effect of spike mutations on SARS-CoV-2 neutralization. Cell Rep 2021; 34:108890. [PMID: 33713594 DOI: 10.1101/2021.01.15.426849] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/17/2021] [Accepted: 03/01/2021] [Indexed: 05/18/2023] Open
Abstract
Multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines show protective efficacy, which is most likely mediated by neutralizing antibodies recognizing the viral entry protein, spike. Because new SARS-CoV-2 variants are emerging rapidly, as exemplified by the B.1.1.7, B.1.351, and P.1 lineages, it is critical to understand whether antibody responses induced by infection with the original SARS-CoV-2 virus or current vaccines remain effective. In this study, we evaluate neutralization of a series of mutated spike pseudotypes based on divergence from SARS-CoV and then compare neutralization of the B.1.1.7 spike pseudotype and individual mutations. Spike-specific monoclonal antibody neutralization is reduced dramatically; in contrast, polyclonal antibodies from individuals infected in early 2020 remain active against most mutated spike pseudotypes, but potency is reduced in a minority of samples. This work highlights that changes in SARS-CoV-2 spike can alter neutralization sensitivity and underlines the need for effective real-time monitoring of emerging mutations and their effect on vaccine efficacy.
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Affiliation(s)
- Chloe Rees-Spear
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Luke Muir
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Sarah A Griffith
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Judith Heaney
- Advanced Pathogens Diagnostic Unit, Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London W1T 4EU, UK
| | - Yoann Aldon
- Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Jonne L Snitselaar
- Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Peter Thomas
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Carl Graham
- School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
| | - Jeffrey Seow
- School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
| | - Nayung Lee
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | | | | | - Catherine F Houlihan
- Advanced Pathogens Diagnostic Unit, Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London W1T 4EU, UK; Research Department of Infection, Division of Infection and Immunity, University College London, London WC1 6BT, UK
| | - Rogier W Sanders
- Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge CB2 0AW, UK
| | | | - Hans J Stauss
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Eleni Nastouli
- Advanced Pathogens Diagnostic Unit, Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London W1T 4EU, UK; The Francis Crick Institute, London NW1 1AT, UK; Great Ormond Street Institute for Child Health, Infection, Immunity and Inflammation, University College London, London WC1N 1EH, UK
| | - Katie J Doores
- School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
| | - Marit J van Gils
- Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Laura E McCoy
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK.
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12
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Hasan A, Al-Ozairi E, Al-Baqsumi Z, Ahmad R, Al-Mulla F. Cellular and Humoral Immune Responses in Covid-19 and Immunotherapeutic Approaches. Immunotargets Ther 2021; 10:63-85. [PMID: 33728277 PMCID: PMC7955763 DOI: 10.2147/itt.s280706] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/22/2020] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (Covid-19), caused by the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), can range in severity from asymptomatic to severe/critical disease. SARS-CoV-2 uses angiotensin-converting enzyme 2 to infect cells leading to a strong inflammatory response, which is most profound in patients who progress to severe Covid-19. Recent studies have begun to unravel some of the differences in the innate and adaptive immune response to SARS-CoV-2 in patients with different degrees of disease severity. These studies have attributed the severe form of Covid-19 to a dysfunctional innate immune response, such as a delayed and/or deficient type I interferon response, coupled with an exaggerated and/or a dysfunctional adaptive immunity. Differences in T-cell (including CD4+ T-cells, CD8+ T-cells, T follicular helper cells, γδ-T-cells, and regulatory T-cells) and B-cell (transitional cells, double-negative 2 cells, antibody-secreting cells) responses have been identified in patients with severe disease compared to mild cases. Moreover, differences in the kinetic/titer of neutralizing antibody responses have been described in severe disease, which may be confounded by antibody-dependent enhancement. Importantly, the presence of preexisting autoantibodies against type I interferon has been described as a major cause of severe/critical disease. Additionally, priorVaccine and multiple vaccine exposure, trained innate immunity, cross-reactive immunity, and serological immune imprinting may all contribute towards disease severity and outcome. Several therapeutic and preventative approaches have been under intense investigations; these include vaccines (three of which have passed Phase 3 clinical trials), therapeutic antibodies, and immunosuppressants.
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Affiliation(s)
- Amal Hasan
- Department of Immunology and Microbiology, Research Division, Dasman Diabetes Institute, Dasman, Kuwait City, Kuwait
| | - Ebaa Al-Ozairi
- Clinical Research Unit, Medical Division, Dasman Diabetes Institute, Dasman, Kuwait City, Kuwait
- Department of Medicine, Faculty of Medicine, Jabriya, Kuwait City, Kuwait
| | - Zahraa Al-Baqsumi
- Department of Immunology and Microbiology, Research Division, Dasman Diabetes Institute, Dasman, Kuwait City, Kuwait
| | - Rasheed Ahmad
- Department of Immunology and Microbiology, Research Division, Dasman Diabetes Institute, Dasman, Kuwait City, Kuwait
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Functional Genomics, Research Division, Dasman Diabetes Institute, Dasman, Kuwait City, Kuwait
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13
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Sajna KV, Kamat S. Antibodies at work in the time of severe acute respiratory syndrome coronavirus 2. Cytotherapy 2021; 23:101-110. [PMID: 32988772 PMCID: PMC7458058 DOI: 10.1016/j.jcyt.2020.08.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/22/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022]
Abstract
In view of devastating effects of COVID-19 on human life, there is an urgent need for the licened vaccines or therapeutics for the SARS-CoV-2 infection. Age-old passive immunization with protective antibodies to neutralize the virus is one of the strategies for emergency prophylaxis and therapy for coronavirus disease 2019 (COVID-19). In this review, the authors discuss up-to-date advances in immune-based therapy for COVID-19. The use of convalescent plasma therapy as the first line of defense to treat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been established, with encouraging results. Monoclonal antibodies (mAbs) that bind to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein or block the interaction between SARS-CoV-2 RBD and the human angiotensin-converting enzyme 2 receptor have been found to be very promising as a countermeasure for tackling the SARS-CoV-2 infection, and clinical trials are underway. Considering the counterproductive antibody-dependent enhancement of the virus, mAbs therapy that is safe and efficacious, even in people with underlying conditions, will be a significant breakthrough. In addition, emerging immunotherapeutic interventions using nanobodies and cellular immunotherapy are promising avenues for tackling the COVID-19 pandemic. The authors also discuss the implication of mAbs as mediators of cytokine storm syndrome to modify the immune response of COVID-19 patients, thus reducing the fatality rate of COVID-19 infection.
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Affiliation(s)
| | - Siya Kamat
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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14
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Sauer MM, Tortorici MA, Park YJ, Walls AC, Homad L, Acton O, Bowen J, Wang C, Xiong X, de van der Schueren W, Quispe J, Hoffstrom BG, Bosch BJ, McGuire AT, Veesler D. Structural basis for broad coronavirus neutralization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.12.29.424482. [PMID: 33398277 PMCID: PMC7781312 DOI: 10.1101/2020.12.29.424482] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Three highly pathogenic β-coronaviruses crossed the animal-to-human species barrier in the past two decades: SARS-CoV, MERS-CoV and SARS-CoV-2. SARS-CoV-2 has infected more than 64 million people worldwide, claimed over 1.4 million lives and is responsible for the ongoing COVID-19 pandemic. We isolated a monoclonal antibody, termed B6, cross-reacting with eight β-coronavirus spike glycoproteins, including all five human-infecting β-coronaviruses, and broadly inhibiting entry of pseudotyped viruses from two coronavirus lineages. Cryo-electron microscopy and X-ray crystallography characterization reveal that B6 binds to a conserved cryptic epitope located in the fusion machinery and indicate that antibody binding sterically interferes with spike conformational changes leading to membrane fusion. Our data provide a structural framework explaining B6 cross-reactivity with β-coronaviruses from three lineages along with proof-of-concept for antibody-mediated broad coronavirus neutralization elicited through vaccination. This study unveils an unexpected target for next-generation structure-guided design of a pan-coronavirus vaccine.
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Affiliation(s)
- Maximilian M. Sauer
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - M. Alexandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institut Pasteur, Unité de Virologie Structurale, Paris, France; CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Leah Homad
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Oliver Acton
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - John Bowen
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Chunyan Wang
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Xiaoli Xiong
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | | | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Benjamin G. Hoffstrom
- Antibody Technology Resource, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Berend-Jan Bosch
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Andrew T. McGuire
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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15
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Forni D, Cagliani R, Pontremoli C, Mozzi A, Pozzoli U, Clerici M, Sironi M. Antigenic variation of SARS-CoV-2 in response to immune pressure. Mol Ecol 2020; 30:3548-3559. [PMID: 33289207 PMCID: PMC7753431 DOI: 10.1111/mec.15730] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/30/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023]
Abstract
Analysis of the bat viruses most closely related to SARS-CoV-2 indicated that the virus probably required limited adaptation to spread in humans. Nonetheless, since its introduction in human populations, SARS-CoV-2 must have been subject to the selective pressure imposed by the human immune system. We exploited the availability of a large number of high-quality SARS-CoV-2 genomes, as well as of validated epitope predictions, to show that B cell epitopes in the spike glycoprotein (S) and in the nucleocapsid protein (N) have higher diversity than nonepitope positions. Similar results were obtained for other human coronaviruses and for sarbecoviruses sampled in bats. Conversely, in the SARS-CoV-2 population, epitopes for CD4+ and CD8+ T cells were not more variable than nonepitope positions. A significant reduction in epitope variability was instead observed for some of the most immunogenic proteins (S, N, ORF8 and ORF3a). Analysis over longer evolutionary time frames indicated that this effect is not due to differential constraints. These data indicate that SARS-CoV-2 evolves to elude the host humoral immune response, whereas recognition by T cells is not actively avoided by the virus. However, we also found a trend of lower diversity of T cell epitopes for common cold coronaviruses, indicating that epitope conservation per se is not directly linked to disease severity. We suggest that conservation serves to maintain epitopes that elicit tolerizing T cell responses or induce T cells with regulatory activity.
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Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEABioinformaticsBosisio PariniItaly
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEABioinformaticsBosisio PariniItaly
| | - Chiara Pontremoli
- Scientific Institute IRCCS E. MEDEABioinformaticsBosisio PariniItaly
| | - Alessandra Mozzi
- Scientific Institute IRCCS E. MEDEABioinformaticsBosisio PariniItaly
| | - Uberto Pozzoli
- Scientific Institute IRCCS E. MEDEABioinformaticsBosisio PariniItaly
| | - Mario Clerici
- Department of Physiopathology and TransplantationUniversity of MilanMilanItaly
- Don C. Gnocchi Foundation ONLUSIRCCSMilanItaly
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEABioinformaticsBosisio PariniItaly
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16
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Ghorbani M, Brooks BR, Klauda JB. Critical Sequence Hotspots for Binding of Novel Coronavirus to Angiotensin Converter Enzyme as Evaluated by Molecular Simulations. J Phys Chem B 2020; 124:10034-10047. [PMID: 33112147 PMCID: PMC7605337 DOI: 10.1021/acs.jpcb.0c05994] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/07/2020] [Indexed: 12/11/2022]
Abstract
The novel coronavirus (nCOV-2019) outbreak has put the world on edge, causing millions of cases and hundreds of thousands of deaths all around the world, as of June 2020, let alone the societal and economic impacts of the crisis. The spike protein of nCOV-2019 resides on the virion's surface mediating coronavirus entry into host cells by binding its receptor binding domain (RBD) to the host cell surface receptor protein, angiotensin converter enzyme (ACE2). Our goal is to provide a detailed structural mechanism of how nCOV-2019 recognizes and establishes contacts with ACE2 and its difference with an earlier severe acute respiratory syndrome coronavirus (SARS-COV) in 2002 via extensive molecular dynamics (MD) simulations. Numerous mutations have been identified in the RBD of nCOV-2019 strains isolated from humans in different parts of the world. In this study, we investigated the effect of these mutations as well as other Ala-scanning mutations on the stability of the RBD/ACE2 complex. It is found that most of the naturally occurring mutations to the RBD either slightly strengthen or have the same binding affinity to ACE2 as the wild-type nCOV-2019. This means that the virus had sufficient binding affinity to its receptor at the beginning of the crisis. This also has implications for any vaccine design endeavors since these mutations could act as antibody escape mutants. Furthermore, in silico Ala-scanning and long-timescale MD simulations highlight the crucial role of the residues at the interface of RBD and ACE2 that may be used as potential pharmacophores for any drug development endeavors. From an evolutional perspective, this study also identifies how the virus has evolved from its predecessor SARS-COV and how it could further evolve to become even more infectious.
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Affiliation(s)
- Mahdi Ghorbani
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
- Laboratory of Computational Biology, National, Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, USA
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National, Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, USA
| | - Jeffery B. Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
- Biophysics Graduate Program, University of Maryland, College Park, MD 20742, USA
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17
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Renn A, Fu Y, Hu X, Hall MD, Simeonov A. Fruitful Neutralizing Antibody Pipeline Brings Hope To Defeat SARS-Cov-2. Trends Pharmacol Sci 2020; 41:815-829. [PMID: 32829936 PMCID: PMC7572790 DOI: 10.1016/j.tips.2020.07.004] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/28/2020] [Accepted: 07/28/2020] [Indexed: 12/24/2022]
Abstract
With the recent spread of severe acute respiratory syndrome coronavirus (SARS-CoV-2)_ infecting >16 million people worldwide as of 28 July 2020, causing >650 000 deaths, there is a desperate need for therapeutic agents and vaccines. Building on knowledge of previous outbreaks of SARS-CoV-1 and Middle East respiratory syndrome (MERS), the development of therapeutic antibodies and vaccines against coronavirus disease 2019 (COVID-19) is taking place at an unprecedented speed. Current efforts towards the development of neutralizing antibodies against COVID-19 are summarized. We also highlight the importance of a fruitful antibody development pipeline to combat the potential escape plans of SARS-CoV-2, including somatic mutations and antibody-dependent enhancement (ADE).
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Affiliation(s)
- Alex Renn
- National Center for Advancing Translational Sciences, National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Ying Fu
- National Center for Advancing Translational Sciences, National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health (NIH), Rockville, MD 20850, USA.
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18
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Guan Q, Sadykov M, Mfarrej S, Hala S, Naeem R, Nugmanova R, Al-Omari A, Salih S, Al Mutair A, Carr MJ, Hall WW, Arold ST, Pain A. A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic. Int J Infect Dis 2020; 100:216-223. [PMID: 32841689 PMCID: PMC7443060 DOI: 10.1016/j.ijid.2020.08.052] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/15/2020] [Accepted: 08/18/2020] [Indexed: 01/20/2023] Open
Abstract
OBJECTIVE The SARS-CoV-2 pathogen has established endemicity in humans. This necessitates the development of rapid genetic surveillance methodologies to serve as an adjunct with existing comprehensive, albeit though slower, genome sequencing-driven approaches. METHODS A total of 21,789 complete genomes were downloaded from GISAID on May 28, 2020 for analyses. We have defined the major clades and subclades of circulating SARS-CoV-2 genomes. A rapid sequencing-based genotyping protocol was developed and tested on SARS-CoV-2-positive RNA samples by next-generation sequencing. RESULTS We describe 11 major mutations which defined five major clades (G614, S84, V251, I378 and D392) of globally circulating viral populations. The clades can specifically identify using an 11-nucleotide genetic barcode. An analysis of amino acid variation in SARS-CoV-2 proteins provided evidence of substitution events in the viral proteins involved in both host entry and genome replication. CONCLUSION Globally circulating SARS-CoV-2 genomes could be classified into 5 major clades based on mutational profiles defined by an 11-nucleotide barcode. We have successfully developed a multiplexed sequencing-based, rapid genotyping protocol for high-throughput classification of major clade types of SARS-CoV-2 in clinical samples. This barcoding strategy will be required to monitor decreases in genetic diversity as treatment and vaccine approaches become widely available.
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Affiliation(s)
- Qingtian Guan
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Mukhtar Sadykov
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Sara Mfarrej
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Sharif Hala
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia; Clinical Microbiology Department, King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Raeece Naeem
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Raushan Nugmanova
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Awad Al-Omari
- School of Medicine, Alfaisal University, Riyadh, Saudi Arabia; Dr.Suliman Al-Habib Medical Group, Riyadh, Saudi Arabia
| | - Samer Salih
- Dr.Suliman Al-Habib Medical Group, Riyadh, Saudi Arabia
| | | | - Michael J Carr
- National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, D04 V1W8, Dublin, Ireland; Research Center for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20 W10 Kita-ku, Sapporo, 001-0020 Japan
| | - William W Hall
- National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, D04 V1W8, Dublin, Ireland; Research Center for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20 W10 Kita-ku, Sapporo, 001-0020 Japan; Global Virus Network (GVN), 801 W. Baltimore St., Baltimore, MD, 21201, USA
| | - Stefan T Arold
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia; Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, 34090 Montpellier, France
| | - Arnab Pain
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia; Research Center for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20 W10 Kita-ku, Sapporo, 001-0020 Japan; Nuffield Division of Clinical Laboratory Sciences (NDCLS), The John Radcliffe Hospital, University of Oxford, Headington, Oxford, OX3 9DU, United Kingdom.
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19
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Alouane T, Laamarti M, Essabbar A, Hakmi M, Bouricha EM, Chemao-Elfihri MW, Kartti S, Boumajdi N, Bendani H, Laamarti R, Ghrifi F, Allam L, Aanniz T, Ouadghiri M, El Hafidi N, El Jaoudi R, Benrahma H, Attar JE, Mentag R, Sbabou L, Nejjari C, Amzazi S, Belyamani L, Ibrahimi A. Genomic Diversity and Hotspot Mutations in 30,983 SARS-CoV-2 Genomes: Moving Toward a Universal Vaccine for the "Confined Virus"? Pathogens 2020; 9:E829. [PMID: 33050463 PMCID: PMC7600297 DOI: 10.3390/pathogens9100829] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic has been ongoing since its onset in late November 2019 in Wuhan, China. Understanding and monitoring the genetic evolution of the virus, its geographical characteristics, and its stability are particularly important for controlling the spread of the disease and especially for the development of a universal vaccine covering all circulating strains. From this perspective, we analyzed 30,983 complete SARS-CoV-2 genomes from 79 countries located in the six continents and collected from 24 December 2019, to 13 May 2020, according to the GISAID database. Our analysis revealed the presence of 3206 variant sites, with a uniform distribution of mutation types in different geographic areas. Remarkably, a low frequency of recurrent mutations has been observed; only 169 mutations (5.27%) had a prevalence greater than 1% of genomes. Nevertheless, fourteen non-synonymous hotspot mutations (>10%) have been identified at different locations along the viral genome; eight in ORF1ab polyprotein (in nsp2, nsp3, transmembrane domain, RdRp, helicase, exonuclease, and endoribonuclease), three in nucleocapsid protein, and one in each of three proteins: Spike, ORF3a, and ORF8. Moreover, 36 non-synonymous mutations were identified in the receptor-binding domain (RBD) of the spike protein with a low prevalence (<1%) across all genomes, of which only four could potentially enhance the binding of the SARS-CoV-2 spike protein to the human ACE2 receptor. These results along with intra-genomic divergence of SARS-CoV-2 could indicate that unlike the influenza virus or HIV viruses, SARS-CoV-2 has a low mutation rate which makes the development of an effective global vaccine very likely.
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Affiliation(s)
- Tarek Alouane
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Meriem Laamarti
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Abdelomunim Essabbar
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Mohammed Hakmi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - El Mehdi Bouricha
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - M. W. Chemao-Elfihri
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Souad Kartti
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Nasma Boumajdi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Houda Bendani
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Rokia Laamarti
- Medical Biotechnology Center, Moroccan Foundation for Science, Innovation & Research (MAScIR), Rabat 10100, Morocco;
| | - Fatima Ghrifi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Loubna Allam
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Tarik Aanniz
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Mouna Ouadghiri
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Naima El Hafidi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Rachid El Jaoudi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
| | - Houda Benrahma
- Faculty of Medicine, Mohammed VI University of Health Sciences (UM6SS), Casablanca 82403, Morocco;
| | - Jalil El Attar
- Riad Laboratory, City Center Hay Riad, Rabat 10112, Morocco;
| | - Rachid Mentag
- Biotechnology Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat 10101, Morocco;
| | - Laila Sbabou
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco;
| | - Chakib Nejjari
- International School of Public Health, Mohammed VI University of Health Sciences (UM6SS), Casablanca 82403, Morocco;
| | - Saaid Amzazi
- Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco;
| | - Lahcen Belyamani
- Emergency Department, Military Hospital Mohammed V, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10112, Morocco;
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco; (M.L.); (A.E.); (M.H.); (E.M.B.); (M.W.C.-E.); (S.K.); (N.B.); (H.B.); (F.G.); (L.A.); (T.A.); (M.O.); (N.E.H.); (R.E.J.)
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20
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Robson B. The use of knowledge management tools in viroinformatics. Example study of a highly conserved sequence motif in Nsp3 of SARS-CoV-2 as a therapeutic target. Comput Biol Med 2020; 125:103963. [PMID: 32828990 PMCID: PMC7424310 DOI: 10.1016/j.compbiomed.2020.103963] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/07/2020] [Accepted: 08/07/2020] [Indexed: 12/16/2022]
Abstract
Knowledge management tools that assist in systematic review and exploration of scientific knowledge generally are of obvious potential importance in evidence based medicine in general, but also to the design of therapeutics based on the protein subsequences and fold motifs of virus proteins as considered here. Rapid access to bundles (clusters) of related elements of knowledge gathered from diverse sources on the Internet and from growing knowledge repositories seem particularly helpful when exploring less obvious therapeutic targets in viruses (for which knowledge new to the researcher is important), and when using the following concept. Subsequences of amino acid residue sequences of proteins that are conserved across strains and species are (a) more likely to be important targets and (b) less likely to exhibit escape mutations that would make them resistant to vaccines and therapeutic agents. However, the terms "conserved" and even "highly conserved" used by authors are matters of degree, depending on how distant from SARS-CoV-2 they wished to go in comparing other sequences. The binding site to the human ACE2 protein as virus receptor and human antibody CR3022 binding site on the spike glycoprotein are rather variable by the criteria used in the present and preceding studies. To look for more strongly conserved targets, open reading frames of SARS-CoV-2 were examined for extremely highly conserved regions, meaning recognizable across many viruses and organisms. Most prominent is a motif found in SARS-CoV-2 non-structural protein 3 (Nsp3). It relates to a fold called type called the macro domain and has remarkably wide distribution across organisms including humans with significant homologies involving three especially conserved subsequences (a) VVVNAANVYLKHGGGVAGALNK, (b) LHVVGPNVNKG, and (c) PLLSAGIFG. Careful study of the variations of these and of the more variable sequences between and around them might provide a finer "scalpel" to ensure inhibition of a vital function of the virus without impairing the functions of related host macro domains.
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Affiliation(s)
- B Robson
- Ingine Inc., Cleveland, OH, USA; The Dirac Foundation, Oxfordshire, UK.
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21
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Dinnon KH, Leist SR, Schäfer A, Edwards CE, Martinez DR, Montgomery SA, West A, Yount BL, Hou YJ, Adams LE, Gully KL, Brown AJ, Huang E, Bryant MD, Choong IC, Glenn JS, Gralinski LE, Sheahan TP, Baric RS. A mouse-adapted model of SARS-CoV-2 to test COVID-19 countermeasures. Nature 2020; 586:560-566. [PMID: 32854108 PMCID: PMC8034761 DOI: 10.1038/s41586-020-2708-8] [Citation(s) in RCA: 475] [Impact Index Per Article: 118.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/20/2020] [Indexed: 12/25/2022]
Abstract
Coronaviruses are prone to transmission to new host species, as recently demonstrated by the spread to humans of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19) pandemic1. Small animal models that recapitulate SARS-CoV-2 disease are needed urgently for rapid evaluation of medical countermeasures2,3. SARS-CoV-2 cannot infect wild-type laboratory mice owing to inefficient interactions between the viral spike protein and the mouse orthologue of the human receptor, angiotensin-converting enzyme 2 (ACE2)4. Here we used reverse genetics5 to remodel the interaction between SARS-CoV-2 spike protein and mouse ACE2 and designed mouse-adapted SARS-CoV-2 (SARS-CoV-2 MA), a recombinant virus that can use mouse ACE2 for entry into cells. SARS-CoV-2 MA was able to replicate in the upper and lower airways of both young adult and aged BALB/c mice. SARS-CoV-2 MA caused more severe disease in aged mice, and exhibited more clinically relevant phenotypes than those seen in Hfh4-ACE2 transgenic mice, which express human ACE2 under the control of the Hfh4 (also known as Foxj1) promoter. We demonstrate the utility of this model using vaccine-challenge studies in immune-competent mice with native expression of mouse ACE2. Finally, we show that the clinical candidate interferon-λ1a (IFN-λ1a) potently inhibits SARS-CoV-2 replication in primary human airway epithelial cells in vitro-both prophylactic and therapeutic administration of IFN-λ1a diminished SARS-CoV-2 replication in mice. In summary, the mouse-adapted SARS-CoV-2 MA model demonstrates age-related disease pathogenesis and supports the clinical use of pegylated IFN-λ1a as a treatment for human COVID-196.
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MESH Headings
- Aging/immunology
- Angiotensin-Converting Enzyme 2
- Animals
- Betacoronavirus/drug effects
- Betacoronavirus/immunology
- Betacoronavirus/pathogenicity
- COVID-19
- COVID-19 Vaccines
- Coronavirus Infections/drug therapy
- Coronavirus Infections/genetics
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Disease Models, Animal
- Female
- Forkhead Transcription Factors/genetics
- Humans
- Interferon-alpha/administration & dosage
- Interferon-alpha/pharmacology
- Interferon-alpha/therapeutic use
- Interferons/administration & dosage
- Interferons/pharmacology
- Interferons/therapeutic use
- Interleukins/administration & dosage
- Interleukins/pharmacology
- Interleukins/therapeutic use
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Transgenic
- Models, Molecular
- Pandemics/prevention & control
- Peptidyl-Dipeptidase A/genetics
- Peptidyl-Dipeptidase A/metabolism
- Pneumonia, Viral/drug therapy
- Pneumonia, Viral/genetics
- Pneumonia, Viral/immunology
- Pneumonia, Viral/prevention & control
- Receptors, Virus/genetics
- Receptors, Virus/metabolism
- SARS-CoV-2
- Viral Vaccines/immunology
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Affiliation(s)
- Kenneth H Dinnon
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Caitlin E Edwards
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David R Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stephanie A Montgomery
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Ande West
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Boyd L Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lily E Adams
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kendra L Gully
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ariane J Brown
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Emily Huang
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | - Jeffrey S Glenn
- Departments of Medicine and Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Palo Alto Veterans Administration, Palo Alto, CA, USA
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ralph S Baric
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina, Chapel Hill, NC, USA.
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22
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Sironi M, Hasnain SE, Rosenthal B, Phan T, Luciani F, Shaw MA, Sallum MA, Mirhashemi ME, Morand S, González-Candelas F. SARS-CoV-2 and COVID-19: A genetic, epidemiological, and evolutionary perspective. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 84:104384. [PMID: 32473976 PMCID: PMC7256558 DOI: 10.1016/j.meegid.2020.104384] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 12/15/2022]
Abstract
In less than five months, COVID-19 has spread from a small focus in Wuhan, China, to more than 5 million people in almost every country in the world, dominating the concern of most governments and public health systems. The social and political distresses caused by this epidemic will certainly impact our world for a long time to come. Here, we synthesize lessons from a range of scientific perspectives rooted in epidemiology, virology, genetics, ecology and evolutionary biology so as to provide perspective on how this pandemic started, how it is developing, and how best we can stop it.
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Affiliation(s)
- Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS E. MEDEA, Bosisio Parini (LC), Italy.
| | - Seyed E Hasnain
- JH Institute of Molecular Medicine, Jamia Hamdard, Tughlakabad, New Delhi, India.
| | - Benjamin Rosenthal
- Animal Parasitic Disease Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA.
| | - Tung Phan
- Division of Clinical Microbiology, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
| | - Fabio Luciani
- University of New South Wales, Sydney, 2052, New South Wales, Australia.
| | - Marie-Anne Shaw
- Leeds Institute of Medical Research at St James's, School of Medicine, University of Leeds, Leeds, United Kingdom.
| | - M Anice Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, Brazil.
| | | | - Serge Morand
- Institute of Evolution Science of Montpellier, Case Courier 064, F-34095 Montpellier, France.
| | - Fernando González-Candelas
- Joint Research Unit Infection and Public Health FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio) and CIBER in Epidemiology and Public Health, Valencia, Spain.
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23
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Lin P, Wang M, Wei Y, Kim T, Wei X. Coronavirus in human diseases: Mechanisms and advances in clinical treatment. MedComm (Beijing) 2020; 1:270-301. [PMID: 33173860 PMCID: PMC7646666 DOI: 10.1002/mco2.26] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 02/05/2023] Open
Abstract
Coronaviruses (CoVs), a subfamily of coronavirinae, are a panel of single-stranded RNA virus. Human coronavirus (HCoV) strains (HCoV-229E, HCoV-OC43, HCoV-HKU1, HCoV-NL63) usually cause mild upper respiratory diseases and are believed to be harmless. However, other HCoVs, associated with severe acute respiratory syndrome, Middle East respiratory syndrome, and COVID-19, have been identified as important pathogens due to their potent infectivity and lethality worldwide. Moreover, currently, no effective antiviral drugs treatments are available so far. In this review, we summarize the biological characters of HCoVs, their association with human diseases, and current therapeutic options for the three severe HCoVs. We also highlight the discussion about novel treatment strategies for HCoVs infections.
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Affiliation(s)
- Panpan Lin
- Laboratory of Aging Research and Cancer Drug Target State Key Laboratory of Biotherapy and Cancer Center National Clinical Research Center for Geriatrics West China Hospital Sichuan University Chengdu China
| | - Manni Wang
- Laboratory of Aging Research and Cancer Drug Target State Key Laboratory of Biotherapy and Cancer Center National Clinical Research Center for Geriatrics West China Hospital Sichuan University Chengdu China
| | - Yuquan Wei
- Laboratory of Aging Research and Cancer Drug Target State Key Laboratory of Biotherapy and Cancer Center National Clinical Research Center for Geriatrics West China Hospital Sichuan University Chengdu China
| | - Taewan Kim
- Wexner Medical Center The Ohio State University Columbus Ohio 43210 USA
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target State Key Laboratory of Biotherapy and Cancer Center National Clinical Research Center for Geriatrics West China Hospital Sichuan University Chengdu China
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24
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Greaney AJ, Starr TN, Gilchuk P, Zost SJ, Binshtein E, Loes AN, Hilton SK, Huddleston J, Eguia R, Crawford KH, Dingens AS, Nargi RS, Sutton RE, Suryadevara N, Rothlauf PW, Liu Z, Whelan SP, Carnahan RH, Crowe JE, Bloom JD. Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.09.10.292078. [PMID: 32935107 PMCID: PMC7491521 DOI: 10.1101/2020.09.10.292078] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Antibodies targeting the SARS-CoV-2 spike receptor-binding domain (RBD) are being developed as therapeutics and make a major contribution to the neutralizing antibody response elicited by infection. Here, we describe a deep mutational scanning method to map how all amino-acid mutations in the RBD affect antibody binding, and apply this method to 10 human monoclonal antibodies. The escape mutations cluster on several surfaces of the RBD that broadly correspond to structurally defined antibody epitopes. However, even antibodies targeting the same RBD surface often have distinct escape mutations. The complete escape maps predict which mutations are selected during viral growth in the presence of single antibodies, and enable us to design escape-resistant antibody cocktails-including cocktails of antibodies that compete for binding to the same surface of the RBD but have different escape mutations. Therefore, complete escape-mutation maps enable rational design of antibody therapeutics and assessment of the antigenic consequences of viral evolution.
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Affiliation(s)
- Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Pavlo Gilchuk
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Seth J. Zost
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Elad Binshtein
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Andrea N. Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Sarah K. Hilton
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - John Huddleston
- Molecular and Cell Biology, University of Washington, Seattle, WA, 98195 USA
| | - Rachel Eguia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Katharine H.D. Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Adam S. Dingens
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Rachel S. Nargi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rachel E. Sutton
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Paul W. Rothlauf
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Program in Virology, Harvard Medical School, Boston, MA, 02115, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Sean P.J. Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Robert H. Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
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25
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Starr TN, Greaney AJ, Hilton SK, Ellis D, Crawford KHD, Dingens AS, Navarro MJ, Bowen JE, Tortorici MA, Walls AC, King NP, Veesler D, Bloom JD. Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding. Cell 2020; 182:1295-1310.e20. [PMID: 32841599 PMCID: PMC7418704 DOI: 10.1016/j.cell.2020.08.012] [Citation(s) in RCA: 1372] [Impact Index Per Article: 343.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/31/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023]
Abstract
The receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein mediates viral attachment to ACE2 receptor and is a major determinant of host range and a dominant target of neutralizing antibodies. Here, we experimentally measure how all amino acid mutations to the RBD affect expression of folded protein and its affinity for ACE2. Most mutations are deleterious for RBD expression and ACE2 binding, and we identify constrained regions on the RBD's surface that may be desirable targets for vaccines and antibody-based therapeutics. But a substantial number of mutations are well tolerated or even enhance ACE2 binding, including at ACE2 interface residues that vary across SARS-related coronaviruses. However, we find no evidence that these ACE2-affinity-enhancing mutations have been selected in current SARS-CoV-2 pandemic isolates. We present an interactive visualization and open analysis pipeline to facilitate use of our dataset for vaccine design and functional annotation of mutations observed during viral surveillance.
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Affiliation(s)
- Tyler N Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Allison J Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Sarah K Hilton
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Daniel Ellis
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
| | - Katharine H D Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Adam S Dingens
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mary Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA.
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26
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A panel of human neutralizing mAbs targeting SARS-CoV-2 spike at multiple epitopes. Nat Commun 2020; 11:4303. [PMID: 32855401 PMCID: PMC7452893 DOI: 10.1038/s41467-020-18159-4] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/05/2020] [Indexed: 12/14/2022] Open
Abstract
The novel highly transmissible human coronavirus SARS-CoV-2 is the causative agent of the COVID-19 pandemic. Thus far, there is no approved therapeutic drug specifically targeting this emerging virus. Here we report the isolation and characterization of a panel of human neutralizing monoclonal antibodies targeting the SARS-CoV-2 receptor binding domain (RBD). These antibodies were selected from a phage display library constructed using peripheral circulatory lymphocytes collected from patients at the acute phase of the disease. These neutralizing antibodies are shown to recognize distinct epitopes on the viral spike RBD. A subset of the antibodies exert their inhibitory activity by abrogating binding of the RBD to the human ACE2 receptor. The human monoclonal antibodies described here represent a promising basis for the design of efficient combined post-exposure therapy for SARS-CoV-2 infection. Here, Noy-Porat, Makdasi et al. report the isolation of a panel of neutralizing mAbs selected against SARS-CoV-2 receptor-binding domain (RBD) from a phage display library constructed based on patient samples collected in the acute phase of the disease, which show efficient neutralizing activities against authentic virus in vitro.
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27
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Somasundaram R, Choraria A, Antonysamy M. An approach towards development of monoclonal IgY antibodies against SARS CoV-2 spike protein (S) using phage display method: A review. Int Immunopharmacol 2020; 85:106654. [PMID: 32512271 PMCID: PMC7266779 DOI: 10.1016/j.intimp.2020.106654] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 01/08/2023]
Abstract
The present state of diagnostic and therapeutic developmental race for vaccines against the SARS CoV-2 (nCOVID-19) focuses on prevention and control of this global pandemic which also represents a critical challenge to the global health community. Although development of novel vaccines can prevent the SARS CoV-2 infections, it is still impeded by several other factors and therefore novel approaches towards treatment and management of this disease is the urgent need. Passive immunotherapy plays a vital role as a possible alternative to meet this challenge and among various antibody sources, chicken egg yolk antibodies (IgY) can be used as an alternative to mammalian antibodies which have been previously studied against SARS CoV outbreak in China. In this review, we discuss the strategies for the use of chicken egg yolk (IgY) antibodies in the development of rapid diagnosis and immunotherapy against SARS CoV-2. Also, IgY antibodies have previously been used against various respiratory bacterial and viral infections in humans and animals. Compared to mammalian antibodies (IgG), chicken egg yolk antibodies (IgY) have greater binding affinity to specific antigens, ease of extraction and lower production costs, hence possessing remarkable pathogen-neutralizing activity of pathogens in respiratory and lungs. We provide an overall importance for the use of monoclonal chicken egg yolk antibodies (IgY) using phage display method describing their potential passive immunotherapeutic application for the treatment and prevention of SARS CoV-2 infection which is simple, fast and safe way of approach for treating patients effectively.
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MESH Headings
- Animals
- Antibodies, Monoclonal/immunology
- Antibodies, Viral/immunology
- Antibody Affinity
- Antibody Specificity
- Betacoronavirus/genetics
- Betacoronavirus/immunology
- COVID-19
- COVID-19 Testing
- Cell Surface Display Techniques
- Chickens
- Clinical Laboratory Techniques
- Coronavirus Infections/diagnosis
- Coronavirus Infections/therapy
- Egg Yolk
- Forecasting
- Humans
- Immunization, Passive
- Immunoglobulins/immunology
- Mammals/immunology
- Models, Molecular
- Pandemics
- Pneumonia, Viral/diagnosis
- Pneumonia, Viral/therapy
- RNA, Viral/genetics
- SARS-CoV-2
- Single-Chain Antibodies/immunology
- Species Specificity
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- COVID-19 Serotherapy
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Affiliation(s)
| | - Ankit Choraria
- Department of Microbiology, PSG College of Arts & Science, Coimbatore, TN, India.
| | - Michael Antonysamy
- Department of Microbiology, PSG College of Arts & Science, Coimbatore, TN, India.
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28
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Ghorbani M, Brooks BR, Klauda JB. Critical Sequence Hot-spots for Binding of nCOV-2019 to ACE2 as Evaluated by Molecular Simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32637962 DOI: 10.1101/2020.06.27.175448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The novel coronavirus (nCOV-2019) outbreak has put the world on edge, causing millions of cases and hundreds of thousands of deaths all around the world, as of June 2020, let alone the societal and economic impacts of the crisis. The spike protein of nCOV-2019 resides on the virion's surface mediating coronavirus entry into host cells by binding its receptor binding domain (RBD) to the host cell surface receptor protein, angiotensin converter enzyme (ACE2). Our goal is to provide a detailed structural mechanism of how nCOV-2019 recognizes and establishes contacts with ACE2 and its difference with an earlier coronavirus SARS-COV in 2002 via extensive molecular dynamics (MD) simulations. Numerous mutations have been identified in the RBD of nCOV-2019 strains isolated from humans in different parts of the world. In this study, we investigated the effect of these mutations as well as other Ala-scanning mutations on the stability of RBD/ACE2 complex. It is found that most of the naturally-occurring mutations to the RBD either strengthen or have the same binding affinity to ACE2 as the wild-type nCOV-2019. This may have implications for high human-to-human transmission of coronavirus in regions where these mutations have been found as well as any vaccine design endeavors since these mutations could act as antibody escape mutants. Furthermore, in-silico Ala-scanning and long-timescale MD simulations, highlight the crucial role of the residues at the interface of RBD and ACE2 that may be used as potential pharmacophores for any drug development endeavors. From an evolutional perspective, this study also identifies how the virus has evolved from its predecessor SARS-COV and how it could further evolve to become more infectious.
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29
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Starr TN, Greaney AJ, Hilton SK, Crawford KH, Navarro MJ, Bowen JE, Tortorici MA, Walls AC, Veesler D, Bloom JD. Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.17.157982. [PMID: 32587970 PMCID: PMC7310626 DOI: 10.1101/2020.06.17.157982] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein mediates viral attachment to ACE2 receptor, and is a major determinant of host range and a dominant target of neutralizing antibodies. Here we experimentally measure how all amino-acid mutations to the RBD affect expression of folded protein and its affinity for ACE2. Most mutations are deleterious for RBD expression and ACE2 binding, and we identify constrained regions on the RBD's surface that may be desirable targets for vaccines and antibody-based therapeutics. But a substantial number of mutations are well tolerated or even enhance ACE2 binding, including at ACE2 interface residues that vary across SARS-related coronaviruses. However, we find no evidence that these ACE2-affinity enhancing mutations have been selected in current SARS-CoV-2 pandemic isolates. We present an interactive visualization and open analysis pipeline to facilitate use of our dataset for vaccine design and functional annotation of mutations observed during viral surveillance.
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Affiliation(s)
- Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Co-first authors
| | - Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
- Co-first authors
| | - Sarah K. Hilton
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Katharine H.D. Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Mary Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
- Lead Contact
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30
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Tay MZ, Poh CM, Rénia L, MacAry PA, Ng LFP. The trinity of COVID-19: immunity, inflammation and intervention. Nat Rev Immunol 2020. [PMID: 32346093 DOI: 10.1038/s41577-010-0311-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the ongoing coronavirus disease 2019 (COVID-19) pandemic. Alongside investigations into the virology of SARS-CoV-2, understanding the fundamental physiological and immunological processes underlying the clinical manifestations of COVID-19 is vital for the identification and rational design of effective therapies. Here, we provide an overview of the pathophysiology of SARS-CoV-2 infection. We describe the interaction of SARS-CoV-2 with the immune system and the subsequent contribution of dysfunctional immune responses to disease progression. From nascent reports describing SARS-CoV-2, we make inferences on the basis of the parallel pathophysiological and immunological features of the other human coronaviruses targeting the lower respiratory tract - severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). Finally, we highlight the implications of these approaches for potential therapeutic interventions that target viral infection and/or immunoregulation.
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Affiliation(s)
- Matthew Zirui Tay
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore, Singapore
| | - Chek Meng Poh
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore, Singapore
| | - Laurent Rénia
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore, Singapore.
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Paul A MacAry
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Lisa F P Ng
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK.
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31
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Tay MZ, Poh CM, Rénia L, MacAry PA, Ng LFP. The trinity of COVID-19: immunity, inflammation and intervention. Nat Rev Immunol 2020; 20:363-374. [PMID: 32346093 PMCID: PMC7187672 DOI: 10.1038/s41577-020-0311-8] [Citation(s) in RCA: 2776] [Impact Index Per Article: 694.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2020] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the ongoing coronavirus disease 2019 (COVID-19) pandemic. Alongside investigations into the virology of SARS-CoV-2, understanding the fundamental physiological and immunological processes underlying the clinical manifestations of COVID-19 is vital for the identification and rational design of effective therapies. Here, we provide an overview of the pathophysiology of SARS-CoV-2 infection. We describe the interaction of SARS-CoV-2 with the immune system and the subsequent contribution of dysfunctional immune responses to disease progression. From nascent reports describing SARS-CoV-2, we make inferences on the basis of the parallel pathophysiological and immunological features of the other human coronaviruses targeting the lower respiratory tract - severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). Finally, we highlight the implications of these approaches for potential therapeutic interventions that target viral infection and/or immunoregulation.
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Affiliation(s)
- Matthew Zirui Tay
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore, Singapore
| | - Chek Meng Poh
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore, Singapore
| | - Laurent Rénia
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore, Singapore.
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Paul A MacAry
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Lisa F P Ng
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK.
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32
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Lango MN. How did we get here? Short history of COVID-19 and other coronavirus-related epidemics. Head Neck 2020; 42:1535-1538. [PMID: 32445249 PMCID: PMC7283747 DOI: 10.1002/hed.26275] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 01/22/2023] Open
Abstract
The COVID‐19 epidemic was not the first coronavirus epidemic of this century and represents one of the increasing number of zoonoses from wildlife to impact global health. SARS CoV‐2, the virus causing the COVID‐19 epidemic is distinct from, but closely resembles SARS CoV‐1, which was responsible for the severe acute respiratory syndrome (SARS) outbreak in 2002. SARS CoV‐1 and 2 share almost 80% of genetic sequences and use the same host cell receptor to initiate viral infection. However, SARS predominantly affected individuals in close contact with infected animals and health care workers. In contrast, CoV‐2 exhibits robust person to person spread, most likely by means of asymptomatic carriers, which has resulted in greater spread of disease, overall morbidity and mortality, despite its lesser virulence. We review recent coronavirus‐related epidemics and distinguish clinical and molecular features of CoV‐2, the causative agent for COVID‐19, and review the current status of vaccine trials.
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Affiliation(s)
- Miriam N Lango
- Department of Head and Neck Surgery, M. D. Anderson Cancer Center, Houston, Texas, USA
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33
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Pinto D, Park YJ, Beltramello M, Walls AC, Tortorici MA, Bianchi S, Jaconi S, Culap K, Zatta F, De Marco A, Peter A, Guarino B, Spreafico R, Cameroni E, Case JB, Chen RE, Havenar-Daughton C, Snell G, Telenti A, Virgin HW, Lanzavecchia A, Diamond MS, Fink K, Veesler D, Corti D. Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature 2020; 583:290-295. [PMID: 32422645 DOI: 10.1038/s41586-020-2349-y] [Citation(s) in RCA: 1374] [Impact Index Per Article: 343.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/12/2020] [Indexed: 12/18/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a newly emerged coronavirus that is responsible for the current pandemic of coronavirus disease 2019 (COVID-19), which has resulted in more than 3.7 million infections and 260,000 deaths as of 6 May 20201,2. Vaccine and therapeutic discovery efforts are paramount to curb the pandemic spread of this zoonotic virus. The SARS-CoV-2 spike (S) glycoprotein promotes entry into host cells and is the main target of neutralizing antibodies. Here we describe several monoclonal antibodies that target the S glycoprotein of SARS-CoV-2, which we identified from memory B cells of an individual who was infected with severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003. One antibody (named S309) potently neutralizes SARS-CoV-2 and SARS-CoV pseudoviruses as well as authentic SARS-CoV-2, by engaging the receptor-binding domain of the S glycoprotein. Using cryo-electron microscopy and binding assays, we show that S309 recognizes an epitope containing a glycan that is conserved within the Sarbecovirus subgenus, without competing with receptor attachment. Antibody cocktails that include S309 in combination with other antibodies that we identified further enhanced SARS-CoV-2 neutralization, and may limit the emergence of neutralization-escape mutants. These results pave the way for using S309 and antibody cocktails containing S309 for prophylaxis in individuals at a high risk of exposure or as a post-exposure therapy to limit or treat severe disease.
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Affiliation(s)
- Dora Pinto
- Humabs BioMed SA, Vir Biotechnology, Bellinzona, Switzerland
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - M Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institut Pasteur and CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Siro Bianchi
- Humabs BioMed SA, Vir Biotechnology, Bellinzona, Switzerland
| | - Stefano Jaconi
- Humabs BioMed SA, Vir Biotechnology, Bellinzona, Switzerland
| | - Katja Culap
- Humabs BioMed SA, Vir Biotechnology, Bellinzona, Switzerland
| | - Fabrizia Zatta
- Humabs BioMed SA, Vir Biotechnology, Bellinzona, Switzerland
| | - Anna De Marco
- Humabs BioMed SA, Vir Biotechnology, Bellinzona, Switzerland
| | - Alessia Peter
- Humabs BioMed SA, Vir Biotechnology, Bellinzona, Switzerland
| | - Barbara Guarino
- Humabs BioMed SA, Vir Biotechnology, Bellinzona, Switzerland
| | | | | | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Rita E Chen
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | | | | | | | | | - Antonio Lanzavecchia
- Humabs BioMed SA, Vir Biotechnology, Bellinzona, Switzerland.,Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.,Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Katja Fink
- Humabs BioMed SA, Vir Biotechnology, Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
| | - Davide Corti
- Humabs BioMed SA, Vir Biotechnology, Bellinzona, Switzerland.
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34
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Mire CE, Chan YP, Borisevich V, Cross RW, Yan L, Agans KN, Dang HV, Veesler D, Fenton KA, Geisbert TW, Broder CC. A Cross-Reactive Humanized Monoclonal Antibody Targeting Fusion Glycoprotein Function Protects Ferrets Against Lethal Nipah Virus and Hendra Virus Infection. J Infect Dis 2020; 221:S471-S479. [PMID: 31686101 PMCID: PMC7199785 DOI: 10.1093/infdis/jiz515] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Nipah virus (NiV) and Hendra virus (HeV) are zoonotic paramyxoviruses that cause severe disease in both animals and humans. There are no approved vaccines or treatments for use in humans; however, therapeutic treatment of both NiV and HeV infection in ferrets and non-human primates with a cross-reactive, neutralizing human monoclonal antibody (mAb), m102.4, targeting the G glycoprotein has been demonstrated. In a previous study, we isolated, characterized, and humanized a cross-reactive, neutralizing anti-F mAb (h5B3.1). The mAb h5B3.1 blocks the required F conformational change needed to facilitate membrane fusion and virus infection, and the epitope recognized by h5B3.1 has been structurally defined; however, the efficacy of h5B3.1 in vivo is unknown. METHODS The post-infection antiviral activity of h5B3.1 was evaluated in vivo by administration in ferrets after NiV and HeV virus challenge. RESULTS All subjects that received h5B3.1 from 1 to several days after infection with a high-dose, oral-nasal virus challenge were protected from disease, whereas all controls died. CONCLUSIONS This is the first successful post-exposure antibody therapy for NiV and HeV using a humanized cross-reactive mAb targeting the F glycoprotein, and the findings suggest that a combination therapy targeting both F and G should be evaluated as a therapy for NiV/HeV infection.
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Affiliation(s)
- Chad E Mire
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Yee-Peng Chan
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Viktoriya Borisevich
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Robert W Cross
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Lianying Yan
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Krystle N Agans
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Ha V Dang
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Karla A Fenton
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Thomas W Geisbert
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Christopher C Broder
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
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35
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Dinnon KH, Leist SR, Schäfer A, Edwards CE, Martinez DR, Montgomery SA, West A, Yount BL, Hou YJ, Adams LE, Gully KL, Brown AJ, Huang E, Bryant MD, Choong IC, Glenn JS, Gralinski LE, Sheahan TP, Baric RS. A mouse-adapted SARS-CoV-2 model for the evaluation of COVID-19 medical countermeasures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.05.06.081497. [PMID: 32511406 PMCID: PMC7263553 DOI: 10.1101/2020.05.06.081497] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Coronaviruses are prone to emergence into new host species most recently evidenced by SARS-CoV-2, the causative agent of the COVID-19 pandemic. Small animal models that recapitulate SARS-CoV-2 disease are desperately needed to rapidly evaluate medical countermeasures (MCMs). SARS-CoV-2 cannot infect wildtype laboratory mice due to inefficient interactions between the viral spike (S) protein and the murine ortholog of the human receptor, ACE2. We used reverse genetics to remodel the S and mACE2 binding interface resulting in a recombinant virus (SARS-CoV-2 MA) that could utilize mACE2 for entry. SARS-CoV-2 MA replicated in both the upper and lower airways of both young adult and aged BALB/c mice. Importantly, disease was more severe in aged mice, and showed more clinically relevant phenotypes than those seen in hACE2 transgenic mice. We then demonstrated the utility of this model through vaccine challenge studies in immune competent mice with native expression of mACE2. Lastly, we show that clinical candidate interferon (IFN) lambda-1a can potently inhibit SARS-CoV-2 replication in primary human airway epithelial cells in vitro , and both prophylactic and therapeutic administration diminished replication in mice. Our mouse-adapted SARS-CoV-2 model demonstrates age-related disease pathogenesis and supports the clinical use of IFN lambda-1a treatment in human COVID-19 infections.
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36
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Kim YS, Lim J, Sung J, Cheong Y, Lee EY, Kim J, Oh H, Kim YS, Cho NH, Choi S, Kang SM, Nam JH, Chae W, Seong BL. Built-in RNA-mediated chaperone (chaperna) for antigen folding tailored to immunized hosts. Biotechnol Bioeng 2020; 117:1990-2007. [PMID: 32297972 PMCID: PMC7262357 DOI: 10.1002/bit.27355] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 01/25/2023]
Abstract
High‐quality antibody (Ab) production depends on the availability of immunologically relevant antigens. We present a potentially universal platform for generating soluble antigens from bacterial hosts, tailored to immunized animals for Ab production. A novel RNA‐dependent chaperone, in which the target antigen is genetically fused with an RNA‐interacting domain (RID) docking tag derived from the immunized host, promotes the solubility and robust folding of the target antigen. We selected the N‐terminal tRNA‐binding domain of lysyl‐tRNA synthetase (LysRS) as the RID for fusion with viral proteins and demonstrated the expression of the RID fusion proteins in their soluble and native conformations; immunization predominantly elicited Ab responses to the target antigen, whereas the “self” RID tag remained nonimmunogenic. Differential immunogenicity of the fusion proteins greatly enriched and simplified the screening of hybridoma clones of monoclonal antibodies (mAbs), enabling specific and sensitive serodiagnosis of MERS‐CoV infection. Moreover, mAbs against the consensus influenza hemagglutinin stalk domain enabled a novel assay for trivalent seasonal influenza vaccines. The Fc‐mediated effector function was demonstrated, which could be harnessed for the design of next‐generation “universal” influenza vaccines. The nonimmunogenic built‐in antigen folding module tailored to a repertoire of immunized animal hosts will drive immunochemical diagnostics, therapeutics, and designer vaccines.
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Affiliation(s)
- Young-Seok Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Jongkwan Lim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Jemin Sung
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Yucheol Cheong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Eun-Young Lee
- Department of Biotechnology, The Catholic University of Korea, Bucheon, Republic of Korea
| | - Jihoon Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Hana Oh
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Yeon-Sook Kim
- Division of Infectious Diseases, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Republic of Korea
| | - Nam-Hyuk Cho
- Department of Microbiology and Immunology, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seongil Choi
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Sang-Moo Kang
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia
| | - Jae-Hwan Nam
- Department of Biotechnology, The Catholic University of Korea, Bucheon, Republic of Korea
| | - Wonil Chae
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Baik L Seong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
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Pinto D, Park YJ, Beltramello M, Walls AC, Tortorici MA, Bianchi S, Jaconi S, Culap K, Zatta F, De Marco A, Peter A, Guarino B, Spreafico R, Cameroni E, Case JB, Chen RE, Havenar-Daughton C, Snell G, Telenti A, Virgin HW, Lanzavecchia A, Diamond MS, Fink K, Veesler D, Corti D. Structural and functional analysis of a potent sarbecovirus neutralizing antibody. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32511354 DOI: 10.1101/2020.04.07.023903] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
SARS-CoV-2 is a newly emerged coronavirus responsible for the current COVID-19 pandemic that has resulted in more than one million infections and 73,000 deaths 1,2 . Vaccine and therapeutic discovery efforts are paramount to curb the pandemic spread of this zoonotic virus. The SARS-CoV-2 spike (S) glycoprotein promotes entry into host cells and is the main target of neutralizing antibodies. Here we describe multiple monoclonal antibodies targeting SARS-CoV-2 S identified from memory B cells of a SARS survivor infected in 2003. One antibody, named S309, potently neutralizes SARS-CoV-2 and SARS-CoV pseudoviruses as well as authentic SARS-CoV-2 by engaging the S receptor-binding domain. Using cryo-electron microscopy and binding assays, we show that S309 recognizes a glycan-containing epitope that is conserved within the sarbecovirus subgenus, without competing with receptor attachment. Antibody cocktails including S309 along with other antibodies identified here further enhanced SARS-CoV-2 neutralization and may limit the emergence of neutralization-escape mutants. These results pave the way for using S309 and S309-containing antibody cocktails for prophylaxis in individuals at high risk of exposure or as a post-exposure therapy to limit or treat severe disease.
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38
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Walls AC, Park YJ, Tortorici MA, Wall A, McGuire AT, Veesler D. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell 2020; 181:281-292.e6. [PMID: 32155444 PMCID: PMC7102599 DOI: 10.1016/j.cell.2020.02.058] [Citation(s) in RCA: 5848] [Impact Index Per Article: 1462.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 10/31/2022]
Abstract
The emergence of SARS-CoV-2 has resulted in >90,000 infections and >3,000 deaths. Coronavirus spike (S) glycoproteins promote entry into cells and are the main target of antibodies. We show that SARS-CoV-2 S uses ACE2 to enter cells and that the receptor-binding domains of SARS-CoV-2 S and SARS-CoV S bind with similar affinities to human ACE2, correlating with the efficient spread of SARS-CoV-2 among humans. We found that the SARS-CoV-2 S glycoprotein harbors a furin cleavage site at the boundary between the S1/S2 subunits, which is processed during biogenesis and sets this virus apart from SARS-CoV and SARS-related CoVs. We determined cryo-EM structures of the SARS-CoV-2 S ectodomain trimer, providing a blueprint for the design of vaccines and inhibitors of viral entry. Finally, we demonstrate that SARS-CoV S murine polyclonal antibodies potently inhibited SARS-CoV-2 S mediated entry into cells, indicating that cross-neutralizing antibodies targeting conserved S epitopes can be elicited upon vaccination.
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Affiliation(s)
- Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - M Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute Pasteur & CNRS UMR 3569, Unité de Virologie Structurale, Paris 75015, France
| | - Abigail Wall
- Vaccines and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA
| | - Andrew T McGuire
- Vaccines and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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39
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Li Z, Tomlinson AC, Wong AH, Zhou D, Desforges M, Talbot PJ, Benlekbir S, Rubinstein JL, Rini JM. The human coronavirus HCoV-229E S-protein structure and receptor binding. eLife 2019; 8:51230. [PMID: 31650956 PMCID: PMC6970540 DOI: 10.7554/elife.51230] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/12/2019] [Indexed: 12/12/2022] Open
Abstract
The coronavirus S-protein mediates receptor binding and fusion of the viral and host cell membranes. In HCoV-229E, its receptor binding domain (RBD) shows extensive sequence variation but how S-protein function is maintained is not understood. Reported are the X-ray crystal structures of Class III-V RBDs in complex with human aminopeptidase N (hAPN), as well as the electron cryomicroscopy structure of the 229E S-protein. The structures show that common core interactions define the specificity for hAPN and that the peripheral RBD sequence variation is accommodated by loop plasticity. The results provide insight into immune evasion and the cross-species transmission of 229E and related coronaviruses. We also find that the 229E S-protein can expose a portion of its helical core to solvent. This is undoubtedly facilitated by hydrophilic subunit interfaces that we show are conserved among coronaviruses. These interfaces likely play a role in the S-protein conformational changes associated with membrane fusion.
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Affiliation(s)
- Zhijie Li
- Department of Molecular Genetics, The University of Toronto, Toronto, Canada
| | | | - Alan Hm Wong
- Department of Biochemistry, The University of Toronto, Toronto, Canada
| | - Dongxia Zhou
- Department of Molecular Genetics, The University of Toronto, Toronto, Canada
| | - Marc Desforges
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, Université du Québec, Laval, Canada
| | - Pierre J Talbot
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, Université du Québec, Laval, Canada
| | - Samir Benlekbir
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - John L Rubinstein
- Department of Biochemistry, The University of Toronto, Toronto, Canada.,Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Medical Biophysics, The University of Toronto, Toronto, Canada
| | - James M Rini
- Department of Molecular Genetics, The University of Toronto, Toronto, Canada.,Department of Biochemistry, The University of Toronto, Toronto, Canada
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40
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An antibody against the F glycoprotein inhibits Nipah and Hendra virus infections. Nat Struct Mol Biol 2019; 26:980-987. [PMID: 31570878 PMCID: PMC6858553 DOI: 10.1038/s41594-019-0308-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 08/21/2019] [Indexed: 12/02/2022]
Abstract
Nipah virus (NiV) and Hendra virus (HeV) are zoonotic henipaviruses (HNVs) responsible for outbreaks of encephalitis and respiratory illness with fatality rates of 50–100%. No vaccines or licensed therapeutics currently exist to protect humans against NiV or HeV. HNVs enter host cells by fusing the viral and cellular membranes via the concerted action of the attachment (G) and fusion (F) glycoproteins, the main targets of the humoral immune response. Here, we describe the isolation and humanization of a potent monoclonal antibody cross-neutralizing NiV and HeV. Cryo-electron microscopy, triggering and fusion studies show the antibody binds to a prefusion-specific quaternary epitope, conserved in NiV F and HeV F glycoproteins, and prevents membrane fusion and viral entry. This work supports the importance of the HNV prefusion F conformation for eliciting a robust immune response and paves the way for using this antibody for prophylaxis and post-exposure therapy with NiV- and HeV-infected individuals. An antibody that recognizes the F glycoproteins from Nipah and Hendra viruses can neutralize both viruses and recognizes a quaternary epitope in the prefusion F trimer, preventing conformational changes required for fusion.
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41
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Kim YS, Aigerim A, Park U, Kim Y, Rhee JY, Choi JP, Park WB, Park SW, Kim Y, Lim DG, Inn KS, Hwang ES, Choi MS, Shin HS, Cho NH. Sequential Emergence and Wide Spread of Neutralization Escape Middle East Respiratory Syndrome Coronavirus Mutants, South Korea, 2015. Emerg Infect Dis 2019; 25:1161-1168. [PMID: 30900977 PMCID: PMC6537729 DOI: 10.3201/eid2506.181722] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The unexpectedly large outbreak of Middle East respiratory syndrome in South Korea in 2015 was initiated by an infected traveler and amplified by several “superspreading” events. Previously, we reported the emergence and spread of mutant Middle East respiratory syndrome coronavirus bearing spike mutations (I529T or D510G) with reduced affinity to human receptor CD26 during the outbreak. To assess the potential association of spike mutations with superspreading events, we collected virus genetic information reported during the outbreak and systemically analyzed the relationship of spike sequences and epidemiology. We found sequential emergence of the spike mutations in 2 superspreaders. In vivo virulence of the mutant viruses seems to decline in human patients, as assessed by fever duration in affected persons. In addition, neutralizing activity against these 2 mutant viruses in serum samples from mice immunized with wild-type spike antigen were gradually reduced, suggesting emergence and wide spread of neutralization escapers during the outbreak.
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42
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Skariyachan S, Challapilli SB, Packirisamy S, Kumargowda ST, Sridhar VS. Recent Aspects on the Pathogenesis Mechanism, Animal Models and Novel Therapeutic Interventions for Middle East Respiratory Syndrome Coronavirus Infections. Front Microbiol 2019; 10:569. [PMID: 30984127 PMCID: PMC6448012 DOI: 10.3389/fmicb.2019.00569] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 03/05/2019] [Indexed: 12/17/2022] Open
Abstract
Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is an emerging zoonotic virus considered as one of the major public threat with a total number of 2 298 laboratory-confirmed cases and 811 associated deaths reported by World Health Organization as of January 2019. The transmission of the virus was expected to be from the camels found in Middle Eastern countries via the animal and human interaction. The genome structure provided information about the pathogenicity and associated virulent factors present in the virus. Recent studies suggested that there were limited insight available on the development of novel therapeutic strategies to induce immunity against the virus. The severities of MERS-CoV infection highlight the necessity of effective approaches for the development of various therapeutic remedies. Thus, the present review comprehensively and critically illustrates the recent aspects on the epidemiology of the virus, the structural and functional features of the viral genome, viral entry and transmission, major mechanisms of pathogenesis and associated virulent factors, current animal models, detection methods and novel strategies for the development of vaccines against MERS-CoV. The review further illustrates the molecular and computational virtual screening platforms which provide insights for the identification of putative drug targets and novel lead molecules toward the development of therapeutic remedies.
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Affiliation(s)
- Sinosh Skariyachan
- R&D Centre, Department of Biotechnology, Dayananda Sagar College of Engineering, Bengaluru, India
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43
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Abstract
Zoonotic viruses circulate as swarms in animal reservoirs and can emerge into human populations, causing epidemics that adversely affect public health. Portable, safe, and effective vaccine platforms are needed in the context of these outbreak and emergence situations. In this work, we report the generation and characterization of an alphavirus replicon vaccine platform based on a non-select agent, attenuated Venezuelan equine encephalitis (VEE) virus vaccine, strain 3526 (VRP 3526). Using both noroviruses and coronaviruses as model systems, we demonstrate the utility of the VRP 3526 platform in the generation of recombinant proteins, production of virus-like particles, and in vivo efficacy as a vaccine against emergent viruses. Importantly, packaging under biosafety level 2 (BSL2) conditions distinguishes VRP 3526 from previously reported alphavirus platforms and makes this approach accessible to the majority of laboratories around the world. In addition, improved outcomes in the vulnerable aged models as well as against heterologous challenge suggest improved efficacy compared to that of previously attenuated VRP approaches. Taking these results together, the VRP 3526 platform represents a safe and highly portable system that can be rapidly deployed under BSL2 conditions for generation of candidate vaccines against emerging microbial pathogens. IMPORTANCE While VEE virus replicon particles provide a robust, established platform for antigen expression and vaccination, its utility has been limited by the requirement for high-containment-level facilities for production and packaging. In this work, we utilize an attenuated vaccine strain capable of use at lower biocontainment level but retaining the capacity of the wild-type replicon particle. Importantly, the new replicon platform provides equal protection for aged mice and following heterologous challenge, which distinguishes it from other attenuated replicon platforms. Together, the new system represents a highly portable, safe system for use in the context of disease emergence.
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44
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Johnson BA, Graham RL, Menachery VD. Viral metagenomics, protein structure, and reverse genetics: Key strategies for investigating coronaviruses. Virology 2017; 517:30-37. [PMID: 29279138 PMCID: PMC5869085 DOI: 10.1016/j.virol.2017.12.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/04/2017] [Accepted: 12/11/2017] [Indexed: 12/25/2022]
Abstract
Viral metagenomics, modeling of protein structure, and manipulation of viral genetics are key approaches that have laid the foundations of our understanding of coronavirus biology. In this review, we discuss the major advances each method has provided and discuss how future studies should leverage these strategies synergistically to answer novel questions.
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Affiliation(s)
- Bryan A Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Rachel L Graham
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
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45
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Wong AHM, Tomlinson ACA, Zhou D, Satkunarajah M, Chen K, Sharon C, Desforges M, Talbot PJ, Rini JM. Receptor-binding loops in alphacoronavirus adaptation and evolution. Nat Commun 2017; 8:1735. [PMID: 29170370 PMCID: PMC5701055 DOI: 10.1038/s41467-017-01706-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 10/06/2017] [Indexed: 02/08/2023] Open
Abstract
RNA viruses are characterized by a high mutation rate, a buffer against environmental change. Nevertheless, the means by which random mutation improves viral fitness is not well characterized. Here we report the X-ray crystal structure of the receptor-binding domain (RBD) of the human coronavirus, HCoV-229E, in complex with the ectodomain of its receptor, aminopeptidase N (APN). Three extended loops are solely responsible for receptor binding and the evolution of HCoV-229E and its close relatives is accompanied by changing loop–receptor interactions. Phylogenetic analysis shows that the natural HCoV-229E receptor-binding loop variation observed defines six RBD classes whose viruses have successively replaced each other in the human population over the past 50 years. These RBD classes differ in their affinity for APN and their ability to bind an HCoV-229E neutralizing antibody. Together, our results provide a model for alphacoronavirus adaptation and evolution based on the use of extended loops for receptor binding. Coronaviruses have a relatively high mutation rate, potentially allowing fast adaptation to changing pressures. Here, Wong et al. provide the structure of the receptor-binding domain (RBD) of the human coronavirus HCoV-229E and its receptor and analyze the evolution of the RBD over the past 50 years.
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Affiliation(s)
- Alan H M Wong
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Aidan C A Tomlinson
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Dongxia Zhou
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Malathy Satkunarajah
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Kevin Chen
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Chetna Sharon
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Marc Desforges
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, Université du Québec, 531 Boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
| | - Pierre J Talbot
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, Université du Québec, 531 Boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
| | - James M Rini
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8. .,Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8.
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46
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Sun Y, Zhang H, Shi J, Zhang Z, Gong R. Identification of a Novel Inhibitor against Middle East Respiratory Syndrome Coronavirus. Viruses 2017; 9:v9090255. [PMID: 28906430 PMCID: PMC5618021 DOI: 10.3390/v9090255] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 12/28/2022] Open
Abstract
The Middle East respiratory syndrome coronavirus (MERS-CoV) was first isolated in 2012, and circulated worldwide with high mortality. The continual outbreaks of MERS-CoV highlight the importance of developing antiviral therapeutics. Here, we rationally designed a novel fusion inhibitor named MERS-five-helix bundle (MERS-5HB) derived from the six-helix bundle (MERS-6HB) which was formed by the process of membrane fusion. MERS-5HB consists of three copies of heptad repeat 1 (HR1) and two copies of heptad repeat 2 (HR2) while MERS-6HB includes three copies each of HR1 and HR2. As it lacks one HR2, MERS-5HB was expected to interact with viral HR2 to interrupt the fusion step. What we found was that MERS-5HB could bind to HR2P, a peptide derived from HR2, with a strong affinity value (KD) of up to 0.24 nM. Subsequent assays indicated that MERS-5HB could inhibit pseudotyped MERS-CoV entry effectively with 50% inhibitory concentration (IC50) of about 1 μM. In addition, MERS-5HB significantly inhibited spike (S) glycoprotein-mediated syncytial formation in a dose-dependent manner. Further biophysical characterization showed that MERS-5HB was a thermo-stable α-helical secondary structure. The inhibitory potency of MERS-5HB may provide an attractive basis for identification of a novel inhibitor against MERS-CoV, as a potential antiviral agent.
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Affiliation(s)
- Yaping Sun
- Center for Emerging Infectious Diseases, CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, No. 44 Xiao Hong Shan, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Huaidong Zhang
- Center for Emerging Infectious Diseases, CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, No. 44 Xiao Hong Shan, Wuhan 430071, China.
| | - Jian Shi
- Center for Emerging Infectious Diseases, CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, No. 44 Xiao Hong Shan, Wuhan 430071, China.
| | - Zhe Zhang
- Center for Emerging Infectious Diseases, CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, No. 44 Xiao Hong Shan, Wuhan 430071, China.
| | - Rui Gong
- Center for Emerging Infectious Diseases, CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, No. 44 Xiao Hong Shan, Wuhan 430071, China.
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47
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Luke T, Wu H, Zhao J, Channappanavar R, Coleman CM, Jiao JA, Matsushita H, Liu Y, Postnikova EN, Ork BL, Glenn G, Flyer D, Defang G, Raviprakash K, Kochel T, Wang J, Nie W, Smith G, Hensley LE, Olinger GG, Kuhn JH, Holbrook MR, Johnson RF, Perlman S, Sullivan E, Frieman MB. Human polyclonal immunoglobulin G from transchromosomic bovines inhibits MERS-CoV in vivo. Sci Transl Med 2016; 8:326ra21. [PMID: 26888429 DOI: 10.1126/scitranslmed.aaf1061] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
As of 13 November 2015, 1618 laboratory-confirmed human cases of Middle East respiratory syndrome coronavirus (MERS-CoV) infection, including 579 deaths, had been reported to the World Health Organization. No specific preventive or therapeutic agent of proven value against MERS-CoV is currently available. Public Health England and the International Severe Acute Respiratory and Emerging Infection Consortium identified passive immunotherapy with neutralizing antibodies as a treatment approach that warrants priority study. Two experimental MERS-CoV vaccines were used to vaccinate two groups of transchromosomic (Tc) bovines that were genetically modified to produce large quantities of fully human polyclonal immunoglobulin G (IgG) antibodies. Vaccination with a clade A γ-irradiated whole killed virion vaccine (Jordan strain) or a clade B spike protein nanoparticle vaccine (Al-Hasa strain) resulted in Tc bovine sera with high enzyme-linked immunosorbent assay (ELISA) and neutralizing antibody titers in vitro. Two purified Tc bovine human IgG immunoglobulins (Tc hIgG), SAB-300 (produced after Jordan strain vaccination) and SAB-301 (produced after Al-Hasa strain vaccination), also had high ELISA and neutralizing antibody titers without antibody-dependent enhancement in vitro. SAB-301 was selected for in vivo and preclinical studies. Administration of single doses of SAB-301 12 hours before or 24 and 48 hours after MERS-CoV infection (Erasmus Medical Center 2012 strain) of Ad5-hDPP4 receptor-transduced mice rapidly resulted in viral lung titers near or below the limit of detection. Tc bovines, combined with the ability to quickly produce Tc hIgG and develop in vitro assays and animal model(s), potentially offer a platform to rapidly produce a therapeutic to prevent and/or treat MERS-CoV infection and/or other emerging infectious diseases.
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Affiliation(s)
- Thomas Luke
- Viral and Rickettsial Diseases Department, Navy Medical Research Center, The Henry Jackson Foundation for the Advancement of Military Medicine, Silver Spring, MD 20910, USA.
| | - Hua Wu
- SAB Biotherapeutics Inc., Sioux Falls, SD 57104, USA
| | - Jincun Zhao
- Department of Microbiology, University of Iowa, Iowa City, IA 52242, USA. State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | | | - Christopher M Coleman
- Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, MD 21201, USA
| | - Jin-An Jiao
- SAB Biotherapeutics Inc., Sioux Falls, SD 57104, USA
| | | | - Ye Liu
- Novavax Inc., Gaithersburg, MD 20878, USA
| | - Elena N Postnikova
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Britini L Ork
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | | | | | - Gabriel Defang
- Department of Virology, Naval Medical Research Unit-3, Cairo FPO AP 09835, Egypt
| | | | - Tadeusz Kochel
- Viral and Rickettsial Diseases Department, Navy Medical Research Center, Silver Spring, MD 20910, USA.
| | - Jonathan Wang
- Thermo Fisher Scientific, South San Francisco, CA 94080, USA
| | - Wensheng Nie
- Thermo Fisher Scientific, South San Francisco, CA 94080, USA
| | - Gale Smith
- Novavax Inc., Gaithersburg, MD 20878, USA
| | - Lisa E Hensley
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Gene G Olinger
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Michael R Holbrook
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Reed F Johnson
- Emerging Viral Pathogens Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Stanley Perlman
- Department of Microbiology, University of Iowa, Iowa City, IA 52242, USA
| | | | - Matthew B Frieman
- Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, MD 21201, USA
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Abstract
Outbreaks from zoonotic sources represent a threat to both human disease as well as the global economy. Despite a wealth of metagenomics studies, methods to leverage these datasets to identify future threats are underdeveloped. In this study, we describe an approach that combines existing metagenomics data with reverse genetics to engineer reagents to evaluate emergence and pathogenic potential of circulating zoonotic viruses. Focusing on the severe acute respiratory syndrome (SARS)-like viruses, the results indicate that the WIV1-coronavirus (CoV) cluster has the ability to directly infect and may undergo limited transmission in human populations. However, in vivo attenuation suggests additional adaptation is required for epidemic disease. Importantly, available SARS monoclonal antibodies offered success in limiting viral infection absent from available vaccine approaches. Together, the data highlight the utility of a platform to identify and prioritize prepandemic strains harbored in animal reservoirs and document the threat posed by WIV1-CoV for emergence in human populations.
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Spread of Mutant Middle East Respiratory Syndrome Coronavirus with Reduced Affinity to Human CD26 during the South Korean Outbreak. mBio 2016; 7:e00019. [PMID: 26933050 PMCID: PMC4810480 DOI: 10.1128/mbio.00019-16] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The newly emerging Middle East respiratory syndrome coronavirus (MERS-CoV) causes a severe respiratory infection with a high mortality rate (~35%). MERS-CoV has been a global threat due to continuous outbreaks in the Arabian peninsula and international spread by infected travelers since 2012. From May to July 2015, a large outbreak initiated by an infected traveler from the Arabian peninsula swept South Korea and resulted in 186 confirmed cases with 38 deaths (case fatality rate, 20.4%). Here, we show the rapid emergence and spread of a mutant MERS-CoV with reduced affinity to the human CD26 receptor during the South Korean outbreak. We isolated 13 new viral genomes from 14 infected patients treated at a hospital and found that 12 of these genomes possess a point mutation in the receptor-binding domain (RBD) of viral spike (S) protein. Specifically, 11 of these genomes have an I529T mutation in RBD, and 1 has a D510G mutation. Strikingly, both mutations result in reduced affinity of RBD to human CD26 compared to wild-type RBD, as measured by surface plasmon resonance analysis and cellular binding assay. Additionally, pseudotyped virus bearing an I529T mutation in S protein showed reduced entry into host cells compared to virus with wild-type S protein. These unexpected findings suggest that MERS-CoV adaptation during human-to-human spread may be driven by host immunological pressure such as neutralizing antibodies, resulting in reduced affinity to host receptor, and thereby impairs viral fitness and virulence, rather than positive selection for a better affinity to CD26. Recently, a large outbreak initiated by an MERS-CoV-infected traveler from the Middle East swept South Korea and resulted in 186 confirmed cases with 38 deaths. This is the largest outbreak outside the Middle East, and it raised strong concerns about the possible emergence of MERS-CoV mutations. Here, we isolated 13 new viral genomes and found that 12 of them possess a point mutation in the receptor-binding domain of viral spike protein, resulting in reduced affinity to the human cognate receptor, CD26, compared to the wild-type virus. These unexpected findings suggest that MERS-CoV adaptation in humans may be driven by host immunological pressure.
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Freund NT, Roitburd-Berman A, Sui J, Marasco WA, Gershoni JM. Reconstitution of the receptor-binding motif of the SARS coronavirus. Protein Eng Des Sel 2015; 28:567-75. [PMID: 26487711 PMCID: PMC7107155 DOI: 10.1093/protein/gzv052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 07/27/2015] [Accepted: 09/08/2015] [Indexed: 12/12/2022] Open
Abstract
The severe acute respiratory syndrome (SARS) coronavirus (CoV) identified in 2003 has infected ∼8000 people worldwide, killing nearly 10% of them. The infection of target cells by the SARS CoV is mediated through the interaction of the viral Spike (S) protein (1255 amino acids) and its cellular receptor, angiotensin-converting enzyme 2 (ACE2). The SARS CoV receptor-binding domain (amino acids N318-T509 of S protein) harbors an extended excursion along its periphery that contacts ACE2 and is designated the receptor-binding motif (RBM, amino acids S432-T486). In addition, the RBM is a major antigenic determinant, able to elicit production of neutralizing antibodies. Hence, the role of the RBM is a bi-functional bioactive surface that can be demonstrated by antibodies such as the neutralizing human anti-SARS monoclonal antibody (mAb) 80R which targets the RBM and competes with the ACE2 receptor for binding. Here, we employ phage-display peptide-libraries to reconstitute a functional RBM. This is achieved by generating a vast collection of candidate RBM peptides that present a diversity of conformations. Screening such 'Conformer Libraries' with corresponding ligands has produced short RBM constructs (ca. 40 amino acids) that can bind both the ACE2 receptor and the neutralizing mAb 80R.
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Affiliation(s)
- Natalia T Freund
- Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel Present address: Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Roitburd-Berman
- Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jianhua Sui
- Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute Department of Medicine, Harvard Medical School, Boston, MA 02115, USA Present address: National Institute of Biological Sciences, Beijing 102206, China
| | - Wayne A Marasco
- Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan M Gershoni
- Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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