601
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Thomson EC, Rosen LE, Shepherd JG, Spreafico R, da Silva Filipe A, Wojcechowskyj JA, Davis C, Piccoli L, Pascall DJ, Dillen J, Lytras S, Czudnochowski N, Shah R, Meury M, Jesudason N, De Marco A, Li K, Bassi J, O'Toole A, Pinto D, Colquhoun RM, Culap K, Jackson B, Zatta F, Rambaut A, Jaconi S, Sreenu VB, Nix J, Zhang I, Jarrett RF, Glass WG, Beltramello M, Nomikou K, Pizzuto M, Tong L, Cameroni E, Croll TI, Johnson N, Di Iulio J, Wickenhagen A, Ceschi A, Harbison AM, Mair D, Ferrari P, Smollett K, Sallusto F, Carmichael S, Garzoni C, Nichols J, Galli M, Hughes J, Riva A, Ho A, Schiuma M, Semple MG, Openshaw PJM, Fadda E, Baillie JK, Chodera JD, Rihn SJ, Lycett SJ, Virgin HW, Telenti A, Corti D, Robertson DL, Snell G. Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell 2021; 184:1171-1187.e20. [PMID: 33621484 PMCID: PMC7843029 DOI: 10.1016/j.cell.2021.01.037] [Citation(s) in RCA: 413] [Impact Index Per Article: 137.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/12/2020] [Accepted: 01/22/2021] [Indexed: 12/13/2022]
Abstract
SARS-CoV-2 can mutate and evade immunity, with consequences for efficacy of emerging vaccines and antibody therapeutics. Here, we demonstrate that the immunodominant SARS-CoV-2 spike (S) receptor binding motif (RBM) is a highly variable region of S and provide epidemiological, clinical, and molecular characterization of a prevalent, sentinel RBM mutation, N439K. We demonstrate N439K S protein has enhanced binding affinity to the hACE2 receptor, and N439K viruses have similar in vitro replication fitness and cause infections with similar clinical outcomes as compared to wild type. We show the N439K mutation confers resistance against several neutralizing monoclonal antibodies, including one authorized for emergency use by the US Food and Drug Administration (FDA), and reduces the activity of some polyclonal sera from persons recovered from infection. Immune evasion mutations that maintain virulence and fitness such as N439K can emerge within SARS-CoV-2 S, highlighting the need for ongoing molecular surveillance to guide development and usage of vaccines and therapeutics.
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Affiliation(s)
- Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK; Department of Clinical Research, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | | | - James G Shepherd
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | | | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | | | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - David J Pascall
- Institute of Biodiversity, Animal Health and Comparative Medicine, Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow G61 1QH, UK
| | - Josh Dillen
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Spyros Lytras
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | | | - Rajiv Shah
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | | | - Natasha Jesudason
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Kathy Li
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Aine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Rachel M Colquhoun
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Vattipally B Sreenu
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Jay Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ivy Zhang
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Ruth F Jarrett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - William G Glass
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Martina Beltramello
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Kyriaki Nomikou
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Matteo Pizzuto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Tristan I Croll
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
| | - Natasha Johnson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | | | - Arthur Wickenhagen
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Alessandro Ceschi
- Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland; Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Sciences of Southern Switzerland, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland; Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Aoife M Harbison
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - Daniel Mair
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Paolo Ferrari
- Department of Nephrology, Ospedale Civico Lugano, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland; Prince of Wales Hospital Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Katherine Smollett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland; ETH Institute of Microbiology, ETH Zurich, 8093 Zürich, Switzerland
| | - Stephen Carmichael
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | - Jenna Nichols
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Massimo Galli
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Agostino Riva
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Marco Schiuma
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7BE, UK; Respiratory Medicine, Alder Hey Children's Hospital, Liverpool L12 2AP, UK
| | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - J Kenneth Baillie
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK; Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh EH16 4SA, UK
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Suzannah J Rihn
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Samantha J Lycett
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Herbert W Virgin
- Vir Biotechnology, San Francisco, CA 94158, USA; Washington University School of Medicine, Saint Louis, MO 63110, USA
| | | | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK.
| | - Gyorgy Snell
- Vir Biotechnology, San Francisco, CA 94158, USA.
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602
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Chung JY, Thone MN, Kwon YJ. COVID-19 vaccines: The status and perspectives in delivery points of view. Adv Drug Deliv Rev 2021; 170:1-25. [PMID: 33359141 PMCID: PMC7759095 DOI: 10.1016/j.addr.2020.12.011] [Citation(s) in RCA: 217] [Impact Index Per Article: 72.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/29/2022]
Abstract
Due to the high prevalence and long incubation periods often without symptoms, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected millions of individuals globally, causing the coronavirus disease 2019 (COVID-19) pandemic. Even with the recent approval of the anti-viral drug, remdesivir, and Emergency Use Authorization of monoclonal antibodies against S protein, bamlanivimab and casirimab/imdevimab, efficient and safe COVID-19 vaccines are still desperately demanded not only to prevent its spread but also to restore social and economic activities via generating mass immunization. Recent Emergency Use Authorization of Pfizer and BioNTech's mRNA vaccine may provide a pathway forward, but monitoring of long-term immunity is still required, and diverse candidates are still under development. As the knowledge of SARS-CoV-2 pathogenesis and interactions with the immune system continues to evolve, a variety of drug candidates are under investigation and in clinical trials. Potential vaccines and therapeutics against COVID-19 include repurposed drugs, monoclonal antibodies, antiviral and antigenic proteins, peptides, and genetically engineered viruses. This paper reviews the virology and immunology of SARS-CoV-2, alternative therapies for COVID-19 to vaccination, principles and design considerations in COVID-19 vaccine development, and the promises and roles of vaccine carriers in addressing the unique immunopathological challenges presented by the disease.
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Affiliation(s)
- Jee Young Chung
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, United States of America
| | - Melissa N Thone
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, United States of America
| | - Young Jik Kwon
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, United States of America; Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697, United States of America; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, United States of America; Department of Biomedical Engineering, University of California, Irvine, CA 92697, United States of America.
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603
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Johnson BA, Xie X, Bailey AL, Kalveram B, Lokugamage KG, Muruato A, Zou J, Zhang X, Juelich T, Smith JK, Zhang L, Bopp N, Schindewolf C, Vu M, Vanderheiden A, Winkler ES, Swetnam D, Plante JA, Aguilar P, Plante KS, Popov V, Lee B, Weaver SC, Suthar MS, Routh AL, Ren P, Ku Z, An Z, Debbink K, Diamond MS, Shi PY, Freiberg AN, Menachery VD. Loss of furin cleavage site attenuates SARS-CoV-2 pathogenesis. Nature 2021; 591:293-299. [PMID: 33494095 PMCID: PMC8175039 DOI: 10.1038/s41586-021-03237-4] [Citation(s) in RCA: 459] [Impact Index Per Article: 153.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/13/2021] [Indexed: 01/22/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-a new coronavirus that has led to a worldwide pandemic1-has a furin cleavage site (PRRAR) in its spike protein that is absent in other group-2B coronaviruses2. To explore whether the furin cleavage site contributes to infection and pathogenesis in this virus, we generated a mutant SARS-CoV-2 that lacks the furin cleavage site (ΔPRRA). Here we report that replicates of ΔPRRA SARS-CoV-2 had faster kinetics, improved fitness in Vero E6 cells and reduced spike protein processing, as compared to parental SARS-CoV-2. However, the ΔPRRA mutant had reduced replication in a human respiratory cell line and was attenuated in both hamster and K18-hACE2 transgenic mouse models of SARS-CoV-2 pathogenesis. Despite reduced disease, the ΔPRRA mutant conferred protection against rechallenge with the parental SARS-CoV-2. Importantly, the neutralization values of sera from patients with coronavirus disease 2019 (COVID-19) and monoclonal antibodies against the receptor-binding domain of SARS-CoV-2 were lower against the ΔPRRA mutant than against parental SARS-CoV-2, probably owing to an increased ratio of particles to plaque-forming units in infections with the former. Together, our results demonstrate a critical role for the furin cleavage site in infection with SARS-CoV-2 and highlight the importance of this site for evaluating the neutralization activities of antibodies.
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Affiliation(s)
- Bryan A Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Adam L Bailey
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Birte Kalveram
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Kumari G Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Antonio Muruato
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xianwen Zhang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Terry Juelich
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jennifer K Smith
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Lihong Zhang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Nathen Bopp
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Craig Schindewolf
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Michelle Vu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Abigail Vanderheiden
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Emma S Winkler
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Daniele Swetnam
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jessica A Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Patricia Aguilar
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Vsevolod Popov
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Benhur Lee
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Mehul S Suthar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Andrew L Routh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ping Ren
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, USA
| | - Kari Debbink
- Department of Natural Sciences Bowie State University, Bowie, MD, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Alexander N Freiberg
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
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604
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Arora P, Pöhlmann S, Hoffmann M. Mutation D614G increases SARS-CoV-2 transmission. Signal Transduct Target Ther 2021; 6:101. [PMID: 33649299 PMCID: PMC7919247 DOI: 10.1038/s41392-021-00502-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 11/09/2022] Open
Affiliation(s)
- Prerna Arora
- Infection Biology Unit, German Primate Center, Göttingen, Germany.,Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany. .,Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany.
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany. .,Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany.
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605
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D614G and SARS-CoV-2 replication fitness. Signal Transduct Target Ther 2021; 6:99. [PMID: 33649290 PMCID: PMC7919242 DOI: 10.1038/s41392-021-00498-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 12/31/2020] [Accepted: 01/18/2021] [Indexed: 12/03/2022] Open
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606
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Mat Yassim AS, Asras MFF, Gazali AM, Marcial-Coba MS, Zainulabid UA, Ahmad HF. COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. MATERIALS TODAY. PROCEEDINGS 2021; 48:828-836. [PMID: 33680867 PMCID: PMC7914017 DOI: 10.1016/j.matpr.2021.02.387] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
SARS-CoV-2 is a very transmissible and pathogenic coronavirus which detected in Malaysia in January 2020. Nevertheless, the sample from Malaysia is still under-sequenced. Hence lacking clarity of the circulating strain in Malaysia leads to a deadlock in understanding the virus infectivity. This study aimed to investigate the genome identity of circulating COVID-19 strains in Pahang and understand disease epidemiology during the pandemic. This study leveraged high-throughput sequencing analysis for the whole genome sequencing and implemented bioinformatic technique for the analysis. Here we reported that the virus with D614G mutation in Spike protein circulates in a few Malaysia states before the Sivagangga cluster announced in Kedah in July 2020. This mutated virus includes our virus sample isolated in April 2020 from an asymptomatic patient in Pahang. Based on the phylogenetic analysis, we discovered the origin of our sample Pahang/IIUM91 was not related to Sivagangga cluster. Here, we have generated 3D structure model of Pahang/IIUM91 Spike protein. D614G mutation in Pahang/IIUM91 Spike protein increases viral stability and flexibility, hence render higher infectivity. Collectively, our results suggest for the establishment of a complete SARS-CoV-2 genome database in Malaysia. Hence, more research should be established to learn the behaviour of this virus.
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Affiliation(s)
- Aini Syahida Mat Yassim
- Faculty Industrial Sciences and Technology, Lebuhraya Tun Razak, 26300 Gambang, Pahang, Malaysia
| | - Mohd Fazli Farida Asras
- Faculty Industrial Sciences and Technology, Lebuhraya Tun Razak, 26300 Gambang, Pahang, Malaysia
| | - Ahmad Mahfuz Gazali
- Faculty Industrial Sciences and Technology, Lebuhraya Tun Razak, 26300 Gambang, Pahang, Malaysia
- Centre for Research in Advanced Tropical Bioscience (Biotropic Centre), Lebuhraya Tun Razak, 26300 Gambang, Pahang, Malaysia
| | | | - Ummu Afeera Zainulabid
- Kulliyyah of Medicine, International Islamic University Malaysia, 25200 Kuantan, Pahang, Malaysia
| | - Hajar Fauzan Ahmad
- Faculty Industrial Sciences and Technology, Lebuhraya Tun Razak, 26300 Gambang, Pahang, Malaysia
- Centre for Research in Advanced Tropical Bioscience (Biotropic Centre), Lebuhraya Tun Razak, 26300 Gambang, Pahang, Malaysia
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607
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Mahat MM, Sabere ASM, Azizi J, Amdan NAN. Potential Applications of Conducting Polymers to Reduce Secondary Bacterial Infections among COVID-19 Patients: a Review. EMERGENT MATERIALS 2021; 4:279-292. [PMID: 33649739 PMCID: PMC7903935 DOI: 10.1007/s42247-021-00188-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/09/2021] [Indexed: 05/02/2023]
Abstract
The COVID-19 pandemic is a motivation for material scientists to search for functional materials with valuable properties to alleviate the risks associated with the coronavirus. The formulation of functional materials requires synergistic understanding on the properties of materials and mechanisms of virus transmission and disease progression, including secondary bacterial infections that are prevalent in COVID-19 patients. A viable candidate in the struggle against the pandemic is antimicrobial polymer, due to their favorable properties of flexibility, lightweight, and ease of synthesis. Polymers are the base material for personal protective equipment (PPE), such as gloves, face mask, face shield, and coverall suit for frontliners. Conducting polymers (CPs) are polymers with electrical properties due to the addition of dopant in the polymer structure. The conductivity of polymers augments their antiviral and antibacterial properties. This review discusses the types of CPs and how their properties could be exploited to ward off bacterial infections in hospital settings, specifically in cases involving COVID-19 patients. This review also covers common CPs fabrication techniques. The key components to produce CPs at several possibilities to fit the current needs in fighting secondary bacterial infections are also discussed.
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Affiliation(s)
- Mohd Muzamir Mahat
- Textile Research Group, Faculty of Applied Sciences, Universiti Teknologi MARA, 40450 Shah Alam, Selangor Malaysia
| | - Awis Sukarni Mohmad Sabere
- Kulliyyah of Pharmacy, International Islamic University Malaysia, Bandar Indera Mahkota, 25200 Kuantan, Pahang Malaysia
| | - Juzaili Azizi
- Centre for Drug Research, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Nur Asyura Nor Amdan
- Bacteriology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Setia Alam, 40170 Shah Alam, Selangor Malaysia
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608
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Yoshimoto FK. A Biochemical Perspective of the Nonstructural Proteins (NSPs) and the Spike Protein of SARS CoV-2. Protein J 2021; 40:260-295. [PMID: 33629236 PMCID: PMC7904240 DOI: 10.1007/s10930-021-09967-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2021] [Indexed: 01/18/2023]
Abstract
The global pandemic that shut down the world in 2020 was caused by the virus, SARS CoV-2. The chemistry of the various nonstructural proteins (NSP3, NSP5, NSP12, NSP13, NSP14, NSP15, NSP16) of SARS CoV-2 is discussed. Secondly, a recent major focus of this pandemic is the variant strains of SARS CoV-2 that are increasingly occurring and more transmissible. One strain, called “D614G”, possesses a glycine (G) instead of an aspartate (D) at position 614 of the spike protein. Additionally, other emerging strains called “501Y.V1” and “501Y.V2” have several differences in the receptor binding domain of the spike protein (N501Y) as well as other locations. These structural changes may enhance the interaction between the spike protein and the ACE2 receptor of the host, increasing infectivity. The global pandemic caused by SARS CoV-2 is a rapidly evolving situation, emphasizing the importance of continuing the efforts to interrogate and understand this virus.
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Affiliation(s)
- Francis K Yoshimoto
- The University of Texas at San Antonio (UTSA), Department of Chemistry, San Antonio, TX, 78249-0698, USA.
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609
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Lee CY, Amrun SN, Chee RS, Goh YS, Mak T, Octavia S, Yeo NK, Chang ZW, Tay MZ, Torres‐Ruesta A, Carissimo G, Poh CM, Fong S, Bei W, Lee S, Young BE, Tan S, Leo Y, Lye DC, Lin RTP, Maurer‐Stroh S, Lee B, Wang C, Renia L, Ng LFP. Human neutralising antibodies elicited by SARS-CoV-2 non-D614G variants offer cross-protection against the SARS-CoV-2 D614G variant. Clin Transl Immunology 2021; 10:e1241. [PMID: 33628442 PMCID: PMC7899292 DOI: 10.1002/cti2.1241] [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] [Received: 11/20/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVES The emergence of a SARS-CoV-2 variant with a point mutation in the spike (S) protein, D614G, has taken precedence over the original Wuhan isolate by May 2020. With an increased infection and transmission rate, it is imperative to determine whether antibodies induced against the D614 isolate may cross-neutralise against the G614 variant. METHODS Antibody profiling against the SARS-CoV-2 S protein of the D614 variant by flow cytometry and assessment of neutralising antibody titres using pseudotyped lentiviruses expressing the SARS-CoV-2 S protein of either the D614 or G614 variant tagged with a luciferase reporter were performed on plasma samples from COVID-19 patients with known D614G status (n = 44 infected with D614, n = 6 infected with G614, n = 7 containing all other clades: O, S, L, V, G, GH or GR). RESULTS Profiling of the anti-SARS-CoV-2 humoral immunity reveals similar neutralisation profiles against both S protein variants, albeit waning neutralising antibody capacity at the later phase of infection. Of clinical importance, patients infected with either the D614 or G614 clade elicited a similar degree of neutralisation against both pseudoviruses, suggesting that the D614G mutation does not impact the neutralisation capacity of the elicited antibodies. CONCLUSIONS Cross-reactivity occurs at the functional level of the humoral response on both the S protein variants, which suggests that existing serological assays will be able to detect both D614 and G614 clades of SARS-CoV-2. More importantly, there should be negligible impact towards the efficacy of antibody-based therapies and vaccines that are currently being developed.
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Affiliation(s)
- Cheryl Yi‐Pin Lee
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Siti Naqiah Amrun
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Rhonda Sin‐Ling Chee
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Yun Shan Goh
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Tze‐Minn Mak
- National Centre for Infectious DiseasesSingapore
- National Public Health LaboratoryNational Centre for Infectious DiseasesSingapore
| | - Sophie Octavia
- National Centre for Infectious DiseasesSingapore
- National Public Health LaboratoryNational Centre for Infectious DiseasesSingapore
| | - Nicholas Kim‐Wah Yeo
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Zi Wei Chang
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Matthew Zirui Tay
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Anthony Torres‐Ruesta
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingapore
| | - Guillaume Carissimo
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Chek Meng Poh
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Siew‐Wai Fong
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
- Department of Biological SciencesNational University of SingaporeSingapore
| | - Wang Bei
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Sandy Lee
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Barnaby Edward Young
- National Centre for Infectious DiseasesSingapore
- Department of Infectious DiseasesTan Tock Seng HospitalSingapore
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingapore
| | - Seow‐Yen Tan
- Department of Infectious DiseasesChangi General HospitalSingapore
| | - Yee‐Sin Leo
- National Centre for Infectious DiseasesSingapore
- Department of Infectious DiseasesTan Tock Seng HospitalSingapore
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingapore
- Yong Loo Lin School of MedicineNational University of Singapore and National University Health SystemSingapore
| | - David C Lye
- National Centre for Infectious DiseasesSingapore
- Department of Infectious DiseasesTan Tock Seng HospitalSingapore
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingapore
- Yong Loo Lin School of MedicineNational University of Singapore and National University Health SystemSingapore
| | - Raymond TP Lin
- National Public Health LaboratoryNational Centre for Infectious DiseasesSingapore
- Department of Microbiology and ImmunologyYong Loo Lin School of MedicineNational University of SingaporeSingapore
| | - Sebastien Maurer‐Stroh
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- National Centre for Infectious DiseasesSingapore
- National Public Health LaboratoryNational Centre for Infectious DiseasesSingapore
- Department of Biological SciencesNational University of SingaporeSingapore
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR)Singapore
| | - Bernett Lee
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Cheng‐I Wang
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Laurent Renia
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Lisa FP Ng
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingapore
- National Institute of Health ResearchHealth Protection Research Unit in Emerging and Zoonotic InfectionsUniversity of LiverpoolLiverpoolUK
- Institute of Infection, Veterinary and Ecological SciencesUniversity of LiverpoolLiverpoolUK
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610
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Hodcroft EB, Domman DB, Snyder DJ, Oguntuyo KY, Van Diest M, Densmore KH, Schwalm KC, Femling J, Carroll JL, Scott RS, Whyte MM, Edwards MW, Hull NC, Kevil CG, Vanchiere JA, Lee B, Dinwiddie DL, Cooper VS, Kamil JP. Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.02.12.21251658. [PMID: 33594385 PMCID: PMC7885944 DOI: 10.1101/2021.02.12.21251658] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein (S) plays critical roles in host cell entry. Non-synonymous substitutions affecting S are not uncommon and have become fixed in a number of SARS-CoV-2 lineages. A subset of such mutations enable escape from neutralizing antibodies or are thought to enhance transmission through mechanisms such as increased affinity for the cell entry receptor, angiotensin-converting enzyme 2 (ACE2). Independent genomic surveillance programs based in New Mexico and Louisiana contemporaneously detected the rapid rise of numerous clade 20G (lineage B.1.2) infections carrying a Q677P substitution in S. The variant was first detected in the US on October 23, yet between 01 Dec 2020 and 19 Jan 2021 it rose to represent 27.8% and 11.3% of all SARS-CoV-2 genomes sequenced from Louisiana and New Mexico, respectively. Q677P cases have been detected predominantly in the south central and southwest United States; as of 03 Feb 2021, GISAID data show 499 viral sequences of this variant from the USA. Phylogenetic analyses revealed the independent evolution and spread of at least six distinct Q677H sub-lineages, with first collection dates ranging from mid-August to late November 2020. Four 677H clades from clade 20G (B.1.2), 20A (B.1.234), and 20B (B.1.1.220, and B.1.1.222) each contain roughly 100 or fewer sequenced cases, while a distinct pair of clade 20G clusters are represented by 754 and 298 cases, respectively. Although sampling bias and founder effects may have contributed to the rise of S:677 polymorphic variants, the proximity of this position to the polybasic cleavage site at the S1/S2 boundary are consistent with its potential functional relevance during cell entry, suggesting parallel evolution of a trait that may confer an advantage in spread or transmission. Taken together, our findings demonstrate simultaneous convergent evolution, thus providing an impetus to further evaluate S:677 polymorphisms for effects on proteolytic processing, cell tropism, and transmissibility.
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Affiliation(s)
- Emma B Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
| | - Daryl B Domman
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Daniel J Snyder
- Microbial Genome Sequencing Center, LLC, Pittsburgh, PA, USA
| | | | - Maarten Van Diest
- Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA
| | - Kenneth H Densmore
- Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA
| | - Kurt C Schwalm
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Jon Femling
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Jennifer L Carroll
- Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA
| | - Rona S Scott
- Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA
| | | | | | - Noah C Hull
- Wyoming Public Health Laboratory, Cheyenne, WY, USA
| | - Christopher G Kevil
- Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA
| | - John A Vanchiere
- Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA
| | - Benhur Lee
- Microbial Genome Sequencing Center, LLC, Pittsburgh, PA, USA
| | | | - Vaughn S Cooper
- University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Jeremy P Kamil
- Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA
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611
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Komiyama M. Molecular-level Anatomy of SARS-CoV-2 for the Battle against COVID-19 Pandemic. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210030] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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612
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Bamberger C, Pankow S, Martínez-Bartolomé S, Diedrich J, Park R, Yates J. The Host Interactome of Spike Expands the Tropism of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.16.431318. [PMID: 33619478 PMCID: PMC7899442 DOI: 10.1101/2021.02.16.431318] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The SARS-CoV-2 virus causes severe acute respiratory syndrome (COVID-19) and has rapidly created a global pandemic. Patients that survive may face a slow recovery with long lasting side effects that can afflict different organs. SARS-CoV-2 primarily infects epithelial airway cells that express the host entry receptor Angiotensin Converting Enzyme 2 (ACE2) which binds to spike protein trimers on the surface of SARS-CoV-2 virions. However, SARS-CoV-2 can spread to other tissues even though they are negative for ACE2. To gain insight into the molecular constituents that might influence SARS-CoV-2 tropism, we determined which additional host factors engage with the viral spike protein in disease-relevant human bronchial epithelial cells (16HBEo-). We found that spike recruited the extracellular proteins laminin and thrombospondin and was retained in the endoplasmatic reticulum (ER) by the proteins DJB11 and FBX2 which support re-folding or degradation of nascent proteins in the ER. Because emerging mutations of the spike protein potentially impact the virus tropism, we compared the interactome of D614 spike with that of the rapidly spreading G614 mutated spike. More D614 than G614 spike associated with the proteins UGGT1, calnexin, HSP7A and GRP78/BiP which ensure glycosylation and folding of proteins in the ER. In contrast to G614 spike, D614 spike was endoproteolytically cleaved, and the N-terminal S1 domain was degraded in the ER even though C-terminal 'S2 only' proteoforms remained present. D614 spike also bound more laminin than G614 spike, which suggested that extracellular laminins may function as co-factor for an alternative, 'S2 only' dependent virus entry. Because the host interactome determines whether an infection is productive, we developed a novel proteome-based cell type set enrichment analysis (pCtSEA). With pCtSEA we determined that the host interactome of the spike protein may extend the tropism of SARS-CoV-2 beyond mucous epithelia to several different cell types, including macrophages and epithelial cells in the nephron. An 'S2 only' dependent, alternative infection of additional cell types with SARS-CoV-2 may impact vaccination strategies and may provide a molecular explanation for a severe or prolonged progression of disease in select COVID-19 patients.
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Affiliation(s)
- Casimir Bamberger
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Sandra Pankow
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Jolene Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Robin Park
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - John Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
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613
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Wang R, Chen J, Gao K, Hozumi Y, Yin C, Wei GW. Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Commun Biol 2021; 4:228. [PMID: 33589648 PMCID: PMC7884689 DOI: 10.1038/s42003-021-01754-6] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 has been mutating since it was first sequenced in early January 2020. Here, we analyze 45,494 complete SARS-CoV-2 geneome sequences in the world to understand their mutations. Among them, 12,754 sequences are from the United States. Our analysis suggests the presence of four substrains and eleven top mutations in the United States. These eleven top mutations belong to 3 disconnected groups. The first and second groups consisting of 5 and 8 concurrent mutations are prevailing, while the other group with three concurrent mutations gradually fades out. Moreover, we reveal that female immune systems are more active than those of males in responding to SARS-CoV-2 infections. One of the top mutations, 27964C > T-(S24L) on ORF8, has an unusually strong gender dependence. Based on the analysis of all mutations on the spike protein, we uncover that two of four SASR-CoV-2 substrains in the United States become potentially more infectious.
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Affiliation(s)
- Rui Wang
- grid.17088.360000 0001 2150 1785Department of Mathematics, Michigan State University, East Lansing, MI 48824 USA
| | - Jiahui Chen
- grid.17088.360000 0001 2150 1785Department of Mathematics, Michigan State University, East Lansing, MI 48824 USA
| | - Kaifu Gao
- grid.17088.360000 0001 2150 1785Department of Mathematics, Michigan State University, East Lansing, MI 48824 USA
| | - Yuta Hozumi
- grid.17088.360000 0001 2150 1785Department of Mathematics, Michigan State University, East Lansing, MI 48824 USA
| | - Changchuan Yin
- grid.185648.60000 0001 2175 0319Department of Mathematics, Statistics, and Computer Science, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - Guo-Wei Wei
- grid.17088.360000 0001 2150 1785Department of Mathematics, Michigan State University, East Lansing, MI 48824 USA ,grid.17088.360000 0001 2150 1785Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824 USA ,grid.17088.360000 0001 2150 1785Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 USA
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614
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Alter G, Gorman M, Patel N, Guebre-Xabier M, Zhu A, Atyeo C, Pullen K, Loos C, Goez-Gazi Y, Carrion R, Tian JH, Yuan D, Bowman K, Zhou B, Maciejewski S, McGrath M, Logue J, Frieman M, Montefiori D, Schendel S, Saphire EO, Lauffenburger D, Greene A, Portnoff A, Massare M, Ellingsworth L, Glenn G, Smith G, Mann C, Amanat F, Krammer F. Collaboration between the Fab and Fc contribute to maximal protection against SARS-CoV-2 following NVX-CoV2373 subunit vaccine with Matrix-M™ vaccination. RESEARCH SQUARE 2021:rs.3.rs-200342. [PMID: 33619473 PMCID: PMC7899467 DOI: 10.21203/rs.3.rs-200342/v1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Recently approved vaccines have already shown remarkable protection in limiting SARS-CoV-2 associated disease. However, immunologic mechanism(s) of protection, as well as how boosting alters immunity to wildtype and newly emerging strains, remain incompletely understood. Here we deeply profiled the humoral immune response in a cohort of non-human primates immunized with a stable recombinant full-length SARS-CoV-2 spike (S) glycoprotein (NVX-CoV2373) at two dose levels, administered as a single or two-dose regimen with a saponin-based adjuvant Matrix-M™. While antigen dose had some effect on Fc-effector profiles, both antigen dose and boosting significantly altered overall titers, neutralization and Fc-effector profiles, driving unique vaccine-induced antibody fingerprints. Combined differences in antibody effector functions and neutralization were strongly associated with distinct levels of protection in the upper and lower respiratory tract, pointing to the presence of combined, but distinct, compartment-specific neutralization and Fc-mechanisms as key determinants of protective immunity against infection. Moreover, NVX-CoV2373 elicited antibodies functionally target emerging SARS-CoV-2 variants, collectively pointing to the critical collaborative role for Fab and Fc in driving maximal protection against SARS-CoV-2. Collectively, the data presented here suggest that a single dose may prevent disease, but that two doses may be essential to block further transmission of SARS-CoV-2 and emerging variants.
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Affiliation(s)
| | | | | | | | - Alex Zhu
- Ragon Institute of MGH, MIT, and Harvard
| | | | | | | | | | | | | | - Dansu Yuan
- Ragon Institute of MGH, MIT, and Harvard
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615
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Li R, Ma X, Deng J, Chen Q, Liu W, Peng Z, Qiao Y, Lin Y, He X, Zhang H. Differential efficiencies to neutralize the novel mutants B.1.1.7 and 501Y.V2 by collected sera from convalescent COVID-19 patients and RBD nanoparticle-vaccinated rhesus macaques. Cell Mol Immunol 2021; 18:1058-1060. [PMID: 33580167 PMCID: PMC7880638 DOI: 10.1038/s41423-021-00641-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 01/19/2021] [Indexed: 12/18/2022] Open
Affiliation(s)
- Rong Li
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Engineering Research Center of Gene Vaccine of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Xiancai Ma
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Engineering Research Center of Gene Vaccine of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Jieyi Deng
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Engineering Research Center of Gene Vaccine of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Qier Chen
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Engineering Research Center of Gene Vaccine of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Weiwei Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Engineering Research Center of Gene Vaccine of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Zhilin Peng
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Engineering Research Center of Gene Vaccine of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Yidan Qiao
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Engineering Research Center of Gene Vaccine of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Yingtong Lin
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Engineering Research Center of Gene Vaccine of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Xin He
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China. .,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China. .,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China. .,Engineering Research Center of Gene Vaccine of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China. .,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China. .,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China. .,Engineering Research Center of Gene Vaccine of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.
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616
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Daniloski Z, Jordan TX, Ilmain JK, Guo X, Bhabha G, tenOever BR, Sanjana NE. The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. eLife 2021; 10:65365. [PMID: 33570490 PMCID: PMC7891930 DOI: 10.7554/elife.65365] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/10/2021] [Indexed: 12/23/2022] Open
Abstract
A novel variant of the SARS-CoV-2 virus carrying a point mutation in the Spike protein (D614G) has recently emerged and rapidly surpassed others in prevalence. This mutation is in linkage disequilibrium with an ORF1b protein variant (P314L), making it difficult to discern the functional significance of the Spike D614G mutation from population genetics alone. Here, we perform site-directed mutagenesis on wild-type human-codon-optimized Spike to introduce the D614G variant. Using multiple human cell lines, including human lung epithelial cells, we found that the lentiviral particles pseudotyped with Spike D614G are more effective at transducing cells than ones pseudotyped with wild-type Spike. The increased transduction with Spike D614G ranged from 1.3- to 2.4-fold in Caco-2 and Calu-3 cells expressing endogenous ACE2 and from 1.5- to 7.7-fold in A549ACE2 and Huh7.5ACE2 overexpressing ACE2. Furthermore, trans-complementation of SARS-CoV-2 virus with Spike D614G showed an increased infectivity in human cells. Although there is minimal difference in ACE2 receptor binding between the D614 and G614 Spike variants, the G614 variant is more resistant to proteolytic cleavage, suggesting a possible mechanism for the increased transduction.
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Affiliation(s)
- Zharko Daniloski
- New York Genome Center, New York, United States.,Department of Biology, New York University, New York, United States
| | - Tristan X Jordan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Juliana K Ilmain
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, United States
| | - Xinyi Guo
- New York Genome Center, New York, United States.,Department of Biology, New York University, New York, United States
| | - Gira Bhabha
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, United States
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Neville E Sanjana
- New York Genome Center, New York, United States.,Department of Biology, New York University, New York, United States
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617
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Devaux CA, Pinault L, Osman IO, Raoult D. Can ACE2 Receptor Polymorphism Predict Species Susceptibility to SARS-CoV-2? Front Public Health 2021; 8:608765. [PMID: 33643982 PMCID: PMC7902720 DOI: 10.3389/fpubh.2020.608765] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/23/2020] [Indexed: 12/16/2022] Open
Abstract
A novel severe acute respiratory syndrome coronavirus, SARS-CoV-2, emerged in China in December 2019 and spread worldwide, causing more than 1.3 million deaths in 11 months. Similar to the human SARS-CoV, SARS-CoV-2 shares strong sequence homologies with a sarbecovirus circulating in Rhinolophus affinis bats. Because bats are expected to be able to transmit their coronaviruses to intermediate animal hosts that in turn are a source of viruses able to cross species barriers and infect humans (so-called spillover model), the identification of an intermediate animal reservoir was the subject of intense researches. It was claimed that a reptile (Ophiophagus hannah) was the intermediate host. This hypothesis was quickly ruled out and replaced by the pangolin (Manis javanica) hypothesis. Yet, pangolin was also recently exonerated from SARS-CoV-2 transmission to humans, leaving other animal species as presumed guilty. Guided by the spillover model, several laboratories investigated in silico the species polymorphism of the angiotensin I converting enzyme 2 (ACE2) to find the best fits with the SARS-CoV-2 spike receptor-binding site. Following the same strategy, we used multi-sequence alignment, 3-D structure analysis, and electrostatic potential surface generation of ACE2 variants to predict their binding capacity to SARS-CoV-2. We report evidence that such simple in silico investigation is a powerful tool to quickly screen which species are potentially susceptible to SARS-CoV-2. However, possible receptor binding does not necessarily lead to successful replication in host. Therefore, we also discuss here the limitations of these in silico approaches in our quest on the origins of COVID-19 pandemic.
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Affiliation(s)
- Christian A. Devaux
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
- CNRS, Marseille, France
| | - Lucile Pinault
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
| | - Ikram Omar Osman
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
- Fondation IHU–Méditerranée Infection, Marseille, France
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618
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Ozono S, Zhang Y, Ode H, Sano K, Tan TS, Imai K, Miyoshi K, Kishigami S, Ueno T, Iwatani Y, Suzuki T, Tokunaga K. SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Nat Commun 2021; 12:848. [PMID: 33558493 PMCID: PMC7870668 DOI: 10.1038/s41467-021-21118-2] [Citation(s) in RCA: 320] [Impact Index Per Article: 106.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 01/14/2021] [Indexed: 12/18/2022] Open
Abstract
The causative agent of the COVID-19 pandemic, SARS-CoV-2, is steadily mutating during continuous transmission among humans. Such mutations can occur in the spike (S) protein that binds to the ACE2 receptor and is cleaved by TMPRSS2. However, whether S mutations affect SARS-CoV-2 cell entry remains unknown. Here, we show that naturally occurring S mutations can reduce or enhance cell entry via ACE2 and TMPRSS2. A SARS-CoV-2 S-pseudotyped lentivirus exhibits substantially lower entry than that of SARS-CoV S. Among S variants, the D614G mutant shows the highest cell entry, as supported by structural and binding analyses. Nevertheless, the D614G mutation does not affect neutralization by antisera against prototypic viruses. Taken together, we conclude that the D614G mutation increases cell entry by acquiring higher affinity to ACE2 while maintaining neutralization susceptibility. Based on these findings, further worldwide surveillance is required to understand SARS-CoV-2 transmissibility among humans.
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Affiliation(s)
- Seiya Ozono
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
- Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi, Japan
| | - Yanzhao Zhang
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hirotaka Ode
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
| | - Kaori Sano
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Toong Seng Tan
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Kazuo Imai
- Self-Defense Forces Central Hospital, Tokyo, Japan
| | | | - Satoshi Kishigami
- Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi, Japan
| | - Takamasa Ueno
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Yasumasa Iwatani
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kenzo Tokunaga
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan.
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619
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Gorman MJ, Patel N, Guebre-Xabier M, Zhu A, Atyeo C, Pullen KM, Loos C, Goez-Gazi Y, Carrion R, Tian JH, Yaun D, Bowman K, Zhou B, Maciejewski S, McGrath ME, Logue J, Frieman MB, Montefiori D, Mann C, Schendel S, Amanat F, Krammer F, Saphire EO, Lauffenburger D, Greene AM, Portnoff AD, Massare MJ, Ellingsworth L, Glenn G, Smith G, Alter G. Collaboration between the Fab and Fc contribute to maximal protection against SARS-CoV-2 in nonhuman primates following NVX-CoV2373 subunit vaccine with Matrix-M™ vaccination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.05.429759. [PMID: 33564763 PMCID: PMC7872351 DOI: 10.1101/2021.02.05.429759] [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
Recently approved vaccines have already shown remarkable protection in limiting SARS-CoV-2 associated disease. However, immunologic mechanism(s) of protection, as well as how boosting alters immunity to wildtype and newly emerging strains, remain incompletely understood. Here we deeply profiled the humoral immune response in a cohort of non-human primates immunized with a stable recombinant full-length SARS-CoV-2 spike (S) glycoprotein (NVX-CoV2373) at two dose levels, administered as a single or two-dose regimen with a saponin-based adjuvant Matrix-M™. While antigen dose had some effect on Fc-effector profiles, both antigen dose and boosting significantly altered overall titers, neutralization and Fc-effector profiles, driving unique vaccine-induced antibody fingerprints. Combined differences in antibody effector functions and neutralization were strongly associated with distinct levels of protection in the upper and lower respiratory tract, pointing to the presence of combined, but distinct, compartment-specific neutralization and Fc-mechanisms as key determinants of protective immunity against infection. Moreover, NVX-CoV2373 elicited antibodies functionally target emerging SARS-CoV-2 variants, collectively pointing to the critical collaborative role for Fab and Fc in driving maximal protection against SARS-CoV-2. Collectively, the data presented here suggest that a single dose may prevent disease, but that two doses may be essential to block further transmission of SARS-CoV-2 and emerging variants. HIGHLIGHTS NVX-CoV2373 subunit vaccine elicits receptor blocking, virus neutralizing antibodies, and Fc-effector functional antibodies.The vaccine protects against respiratory tract infection and virus shedding in non-human primates (NHPs).Both neutralizing and Fc-effector functions contribute to protection, potentially through different mechanisms in the upper and lower respiratory tract.Both macaque and human vaccine-induced antibodies exhibit altered Fc-receptor binding to emerging mutants.
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Affiliation(s)
- Matthew J Gorman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Nita Patel
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | | | - Alex Zhu
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Krista M Pullen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Carolin Loos
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yenny Goez-Gazi
- Texas Biomedical Research Institute. 8715 West Military Drive, San Antonio, TX 78227, USA
| | - Ricardo Carrion
- Texas Biomedical Research Institute. 8715 West Military Drive, San Antonio, TX 78227, USA
| | - Jing-Hui Tian
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | - Dansu Yaun
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Kathryn Bowman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Bin Zhou
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | | | - Marisa E McGrath
- University of Maryland, School of Medicine, 685 West Baltimore St, Baltimore, MD 21201, USA
| | - James Logue
- University of Maryland, School of Medicine, 685 West Baltimore St, Baltimore, MD 21201, USA
| | - Matthew B Frieman
- University of Maryland, School of Medicine, 685 West Baltimore St, Baltimore, MD 21201, USA
| | - David Montefiori
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Colin Mann
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | | | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Douglas Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ann M Greene
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | | | | | | | - Gregory Glenn
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | - Gale Smith
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
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620
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Badaoui B, Sadki K, Talbi C, Salah D, Tazi L. Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. BIOSAFETY AND HEALTH 2021; 3:124-127. [PMID: 33558859 PMCID: PMC7857134 DOI: 10.1016/j.bsheal.2021.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 01/18/2021] [Accepted: 01/29/2021] [Indexed: 12/31/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), declared as a pandemic due to its rapid spread worldwide. In this study, we investigate the genetic diversity and genomic epidemiology of SARS-CoV-2, using 22 virus genome sequences reported by three different laboratories in Morocco till June 7,2020, as well as 40,366 virus genomes from all around the world. The SARS-CoV-2 genomes from Moroccan patients revealed 62 mutations, of which 30 were mis-sense mutations. The mutations Spike_D614G and NSP12_P323L were present in all the 22 analyzed sequences, followed by N_G204R and N_R203K, which occurred in 9 among the 22 sequences. The mutations NSP10_R134S, NSP15_D335N, NSP16_I169L, NSP3_L431H, NSP3_P1292L and Spike_V6F occurred once in Moroccan sequences, with no record in other sequences worldwide. Phylogenetic analyses revealed that Moroccan SARS-CoV-2 genomes included 9 viruses belonging to Clade 20A, 9 to Clade 20B and 2 to Clade 20C, suggesting that the epidemic spread in Morocco did not display a predominant SARS-CoV-2 route. Therefore, multiple and unrelated introductions of SARS-CoV-2 into Morocco through different routes have occurred, giving rise to the diversity of virus genomes in the country. Further, in all probability, the SARS-CoV-2 circulated in a cryptic way in Morocco, starting from January 15, 2020 before the first case was officially discovered on March 2, 2020.
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Affiliation(s)
| | - Khalid Sadki
- Faculty of Sciences, Mohamed V University in Rabat, Morocco
| | - Chouhra Talbi
- Faculty of Sciences, Mohamed V University in Rabat, Morocco
| | - Driss Salah
- Faculty of Sciences, Mohamed V University in Rabat, Morocco
| | - Lina Tazi
- Faculty of Sciences, Mohamed V University in Rabat, Morocco
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621
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Beltrán-Pavez C, Riquelme-Barrios S, Oyarzún-Arrau A, Gaete-Argel A, González-Stegmaier R, Cereceda-Solis K, Aguirre A, Travisany D, Palma-Vejares R, Barriga GP, Gaggero A, Martínez-Valdebenito C, Corre NL, Ferrés M, Balcells ME, Fernandez J, Ramírez E, Villarroel F, Valiente-Echeverría F, Soto-Rifo R. Insights into neutralizing antibody responses in individuals exposed to SARS-CoV-2 in Chile. SCIENCE ADVANCES 2021; 7:eabe6855. [PMID: 33579701 PMCID: PMC7880587 DOI: 10.1126/sciadv.abe6855] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/23/2020] [Indexed: 05/08/2023]
Abstract
Chile has one of the worst numbers worldwide in terms of SARS-CoV-2 positive cases and COVID-19-related deaths per million inhabitants; thus, characterization of neutralizing antibody (NAb) responses in the general population is critical to understanding of immunity at the local level. Given our inability to perform massive classical neutralization assays due to the scarce availability of BSL-3 facilities in the country, we developed and fully characterized an HIV-based SARS-CoV-2 pseudotype, which was used in a 96-well plate format to investigate NAb responses in samples from individuals exposed to SARS-CoV-2 or treated with convalescent plasma. We also identified samples with decreased or enhanced neutralization activity against the D614G spike variant compared with the wild type, indicating the relevance of this variant in host immunity. The data presented here represent the first insights into NAb responses in individuals from Chile, serving as a guide for future studies in the country.
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Affiliation(s)
- Carolina Beltrán-Pavez
- SARS-CoV-2 Research Group, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Sebastián Riquelme-Barrios
- SARS-CoV-2 Research Group, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Aarón Oyarzún-Arrau
- SARS-CoV-2 Research Group, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Aracelly Gaete-Argel
- SARS-CoV-2 Research Group, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | | | - Karina Cereceda-Solis
- Translational Medicine Laboratory, Fundación Arturo López Pérez Cancer Center, Santiago, Chile
| | - Adam Aguirre
- Translational Medicine Laboratory, Fundación Arturo López Pérez Cancer Center, Santiago, Chile
| | - Dante Travisany
- Centro de Modelamiento Matemático UMI-CNRS 2807, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile and Fondap Center for Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- INRIA Chile Research Center, Santiago, Chile
| | - Ricardo Palma-Vejares
- Centro de Modelamiento Matemático UMI-CNRS 2807, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile and Fondap Center for Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Gonzalo P Barriga
- SARS-CoV-2 Research Group, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Laboratory of Emerging Viruses, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Aldo Gaggero
- SARS-CoV-2 Research Group, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Laboratory of Environmental Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Constanza Martínez-Valdebenito
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, División de Pediatría, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Laboratorio de Infectología y Virología Molecular, Laboratorio de Bioseguridad Nivel 3, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nicole Le Corre
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, División de Pediatría, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Laboratorio de Infectología y Virología Molecular, Laboratorio de Bioseguridad Nivel 3, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcela Ferrés
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, División de Pediatría, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Laboratorio de Infectología y Virología Molecular, Laboratorio de Bioseguridad Nivel 3, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - María Elvira Balcells
- Departamento de Enfermedades Infecciosas del Adulto, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jorge Fernandez
- Subdepartamento de Genética Molecular, Instituto de Salud Pública, Santiago, Chile
| | - Eugenio Ramírez
- Sección Virus Oncogénicos, Subdepartamento de Enfermedades Virales, Instituto de Salud Pública, Santiago, Chile
| | - Franz Villarroel
- Translational Medicine Laboratory, Fundación Arturo López Pérez Cancer Center, Santiago, Chile
| | - Fernando Valiente-Echeverría
- SARS-CoV-2 Research Group, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Ricardo Soto-Rifo
- SARS-CoV-2 Research Group, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
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622
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Jackson CB, Zhang L, Farzan M, Choe H. Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Biochem Biophys Res Commun 2021; 538:108-115. [PMID: 33220921 PMCID: PMC7664360 DOI: 10.1016/j.bbrc.2020.11.026] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 11/09/2020] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped virus which binds its cellular receptor angiotensin-converting enzyme 2 (ACE2) and enters hosts cells through the action of its spike (S) glycoprotein displayed on the surface of the virion. Compared to the reference strain of SARS-CoV-2, the majority of currently circulating isolates possess an S protein variant characterized by an aspartic acid-to-glycine substitution at amino acid position 614 (D614G). Residue 614 lies outside the receptor binding domain (RBD) and the mutation does not alter the affinity of monomeric S protein for ACE2. However, S(G614), compared to S(D614), mediates more efficient ACE2-mediated transduction of cells by S-pseudotyped vectors and more efficient infection of cells and animals by live SARS-CoV-2. This review summarizes and synthesizes the epidemiological and functional observations of the D614G spike mutation, with focus on the biochemical and cell-biological impact of this mutation and its consequences for S protein function. We further discuss the significance of these recent findings in the context of the current global pandemic.
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Affiliation(s)
- Cody B Jackson
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA.
| | - Lizhou Zhang
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Michael Farzan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Hyeryun Choe
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
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623
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Suzuki K, Okada H, Tomita H, Sumi K, Kakino Y, Yasuda R, Kitagawa Y, Fukuta T, Miyake T, Yoshida S, Suzuki A, Ogura S. Possible involvement of Syndecan-1 in the state of COVID-19 related to endothelial injury. Thromb J 2021; 19:5. [PMID: 33504351 PMCID: PMC7838859 DOI: 10.1186/s12959-021-00258-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/13/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The coronavirus infection 2019 (COVID-19) is associated with microvascular endothelial injury. Here, we report that syndecan-1, a component of endothelial glycocalyx, may reflect the disease state of COVID-19 related to endothelial injury. CASE PRESENTATION A patient with COVID-19 was transferred to the intensive care unit of our hospital. Computed tomography of the chest showed bilateral ground glass opacities, which was diagnosed as acute respiratory syndrome. The PaO2/FIO2 ratio gradually increased from 158 on hospitalization to 300 on Day 11, on which day the ventilator was withdrawn. However, serum syndecan-1 (SDC-1) level gradually decreased from 400.5 ng/ml at hospitalization to 165.1 ng/ml on Day 5. On Day 6, serum SDC-1 level increased to 612.9 ng/ml owing to a systemic thrombosis with an increase in D-dimer. Serum SDC-1 level then decreased until 206.0 ng/ml on Day 11 after a decrease in D-dimer. The patient was transferred to another hospital on Day 21 after hospitalization. CONCLUSIONS In this case report, changes in serum SDC-1 level closely reflected the change in disease condition in a patient with COVID-19. Serum SDC-1 may be a useful biomarker for monitoring the disease state of critically ill patients with COVID-19.
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Affiliation(s)
- Keiko Suzuki
- Department of Pharmacy, Gifu University Hospital, Gifu, Japan
| | - Hideshi Okada
- Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu, 501-1194, Japan.
| | - Hiroyuki Tomita
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Kazuyuki Sumi
- Department of Pharmacy, Gifu University Hospital, Gifu, Japan
| | - Yoshinori Kakino
- Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu, 501-1194, Japan
| | - Ryu Yasuda
- Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu, 501-1194, Japan
| | - Yuichiro Kitagawa
- Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu, 501-1194, Japan
| | - Tetsuya Fukuta
- Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu, 501-1194, Japan
| | - Takahito Miyake
- Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu, 501-1194, Japan
| | - Shozo Yoshida
- Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu, 501-1194, Japan
| | - Akio Suzuki
- Department of Pharmacy, Gifu University Hospital, Gifu, Japan
| | - Shinji Ogura
- Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu, 501-1194, Japan
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624
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Barrett CT, Neal HE, Edmonds K, Moncman CL, Thompson R, Branttie JM, Boggs KB, Wu CY, Leung DW, Dutch RE. Effect of mutations in the SARS-CoV-2 spike protein on protein stability, cleavage, and cell-cell fusion function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.24.428007. [PMID: 33532777 PMCID: PMC7852270 DOI: 10.1101/2021.01.24.428007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The SARS-CoV-2 spike protein (S) is the sole viral protein responsible for both viral binding to a host cell and the membrane fusion event needed for cell entry. In addition to facilitating fusion needed for viral entry, S can also drive cell-cell fusion, a pathogenic effect observed in the lungs of SARS-CoV-2 infected patients. While several studies have investigated S requirements involved in viral particle entry, examination of S stability and factors involved in S cell-cell fusion remain limited. We demonstrate that S must be processed at the S1/S2 border in order to mediate cell-cell fusion, and that mutations at potential cleavage sites within the S2 subunit alter S processing at the S1/S2 border, thus preventing cell-cell fusion. We also identify residues within the internal fusion peptide and the cytoplasmic tail that modulate S cell-cell fusion. Additionally, we examine S stability and protein cleavage kinetics in a variety of mammalian cell lines, including a bat cell line related to the likely reservoir species for SARS-CoV-2, and provide evidence that proteolytic processing alters the stability of the S trimer. This work therefore offers insight into S stability, proteolytic processing, and factors that mediate S cell-cell fusion, all of which help give a more comprehensive understanding of this highly sought-after therapeutic target.
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Affiliation(s)
- Chelsea T. Barrett
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Hadley E. Neal
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Kearstin Edmonds
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Carole L. Moncman
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Rachel Thompson
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Jean M. Branttie
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Kerri Beth Boggs
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Cheng-Yu Wu
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Daisy W. Leung
- Division of Infection Diseases, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Rebecca E. Dutch
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
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625
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Guthmiller JJ, Stovicek O, Wang J, Changrob S, Li L, Halfmann P, Zheng NY, Utset H, Stamper CT, Dugan HL, Miller WD, Huang M, Dai YN, Nelson CA, Hall PD, Jansen M, Shanmugarajah K, Donington JS, Krammer F, Fremont DH, Joachimiak A, Kawaoka Y, Tesic V, Madariaga ML, Wilson PC. SARS-CoV-2 Infection Severity Is Linked to Superior Humoral Immunity against the Spike. mBio 2021; 12:e02940-20. [PMID: 33468695 PMCID: PMC7845638 DOI: 10.1128/mbio.02940-20] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/16/2020] [Indexed: 12/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently causing a global pandemic. The antigen specificity of the antibody response mounted against this novel virus is not understood in detail. Here, we report that subjects with a more severe SARS-CoV-2 infection exhibit a larger antibody response against the spike and nucleocapsid protein and epitope spreading to subdominant viral antigens, such as open reading frame 8 and nonstructural proteins. Subjects with a greater antibody response mounted a larger memory B cell response against the spike, but not the nucleocapsid protein. Additionally, we revealed that antibodies against the spike are still capable of binding the D614G spike mutant and cross-react with the SARS-CoV-1 receptor binding domain. Together, this study reveals that subjects with a more severe SARS-CoV-2 infection exhibit a greater overall antibody response to the spike and nucleocapsid protein and a larger memory B cell response against the spike.IMPORTANCE With the ongoing pandemic, it is critical to understand how natural immunity against SARS-CoV-2 and COVID-19 develops. We have identified that subjects with more severe COVID-19 disease mount a more robust and neutralizing antibody response against SARS-CoV-2 spike protein. Subjects who mounted a larger response against the spike also mounted antibody responses against other viral antigens, including the nucleocapsid protein and ORF8. Additionally, this study reveals that subjects with more severe disease mount a larger memory B cell response against the spike. These data suggest that subjects with more severe COVID-19 disease are likely better protected from reinfection with SARS-CoV-2.
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Affiliation(s)
- Jenna J Guthmiller
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, Illinois, USA
| | - Olivia Stovicek
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, Illinois, USA
| | - Jiaolong Wang
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, Illinois, USA
| | - Siriruk Changrob
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, Illinois, USA
| | - Lei Li
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, Illinois, USA
| | - Peter Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nai-Ying Zheng
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, Illinois, USA
| | - Henry Utset
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, Illinois, USA
| | | | - Haley L Dugan
- Committee on Immunology, University of Chicago, Chicago, Illinois, USA
| | - William D Miller
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois, USA
| | - Min Huang
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, Illinois, USA
| | - Ya-Nan Dai
- Department of Pathology and Immunology and Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Christopher A Nelson
- Department of Pathology and Immunology and Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Paige D Hall
- Department of Pathology and Immunology and Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Maud Jansen
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | | | | | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Daved H Fremont
- Department of Pathology and Immunology and Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Vera Tesic
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
| | | | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, Illinois, USA
- Committee on Immunology, University of Chicago, Chicago, Illinois, USA
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626
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Watanabe Y, Mendonça L, Allen ER, Howe A, Lee M, Allen JD, Chawla H, Pulido D, Donnellan F, Davies H, Ulaszewska M, Belij-Rammerstorfer S, Morris S, Krebs AS, Dejnirattisai W, Mongkolsapaya J, Supasa P, Screaton GR, Green CM, Lambe T, Zhang P, Gilbert SC, Crispin M. Native-like SARS-CoV-2 spike glycoprotein expressed by ChAdOx1 nCoV-19/AZD1222 vaccine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.15.426463. [PMID: 33501433 PMCID: PMC7836103 DOI: 10.1101/2021.01.15.426463] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Vaccine development against the SARS-CoV-2 virus focuses on the principal target of the neutralizing immune response, the spike (S) glycoprotein. Adenovirus-vectored vaccines offer an effective platform for the delivery of viral antigen, but it is important for the generation of neutralizing antibodies that they produce appropriately processed and assembled viral antigen that mimics that observed on the SARS-CoV-2 virus. Here, we describe the structure, conformation and glycosylation of the S protein derived from the adenovirus-vectored ChAdOx1 nCoV-19/AZD1222 vaccine. We demonstrate native-like post-translational processing and assembly, and reveal the expression of S proteins on the surface of cells adopting the trimeric prefusion conformation. The data presented here confirms the use of ChAdOx1 adenovirus vectors as a leading platform technology for SARS-CoV-2 vaccines.
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Affiliation(s)
- Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Luiza Mendonça
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Elizabeth R. Allen
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew Howe
- Electron Bio-imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Mercede Lee
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Himanshi Chawla
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - David Pulido
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Francesca Donnellan
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Hannah Davies
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Marta Ulaszewska
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sandra Belij-Rammerstorfer
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susan Morris
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anna-Sophia Krebs
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Wanwisa Dejnirattisai
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Juthathip Mongkolsapaya
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Dengue Hemorrhagic Fever Research Unit, Office for Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Chinese Academy of Medical Science(CAMS) Oxford Institute (COI), University of Oxford, Oxford, U.K
| | - Piyada Supasa
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Gavin R. Screaton
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Division of Medical Sciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Catherine M. Green
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Teresa Lambe
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Peijun Zhang
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
- Electron Bio-imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Sarah C. Gilbert
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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627
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Everett HE, Lean FZX, Byrne AMP, van Diemen PM, Rhodes S, James J, Mollett B, Coward VJ, Skinner P, Warren CJ, Bewley KR, Watson S, Hurley S, Ryan KA, Hall Y, Simmons H, Núñez A, Carroll MW, Brown IH, Brookes SM. Intranasal Infection of Ferrets with SARS-CoV-2 as a Model for Asymptomatic Human Infection. Viruses 2021; 13:113. [PMID: 33467732 PMCID: PMC7830262 DOI: 10.3390/v13010113] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/07/2021] [Accepted: 01/10/2021] [Indexed: 02/07/2023] Open
Abstract
Ferrets were experimentally inoculated with SARS-CoV-2 (severe acute respiratory syndrome (SARS)-related coronavirus 2) to assess infection dynamics and host response. During the resulting subclinical infection, viral RNA was monitored between 2 and 21 days post-inoculation (dpi), and reached a peak in the upper respiratory cavity between 4 and 6 dpi. Viral genomic sequence analysis in samples from three animals identified the Y453F nucleotide substitution relative to the inoculum. Viral RNA was also detected in environmental samples, specifically in swabs of ferret fur. Microscopy analysis revealed viral protein and RNA in upper respiratory tract tissues, notably in cells of the respiratory and olfactory mucosae of the nasal turbinates, including olfactory neuronal cells. Antibody responses to the spike and nucleoprotein were detected from 21 dpi, but virus-neutralizing activity was low. A second intranasal inoculation (re-exposure) of two ferrets after a 17-day interval did not produce re-initiation of viral RNA shedding, but did amplify the humoral response in one animal. Therefore, ferrets can be experimentally infected with SARS-CoV-2 to model human asymptomatic infection.
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Affiliation(s)
- Helen E. Everett
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Fabian Z. X. Lean
- Pathology and Animal Sciences Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (F.Z.X.L.); (S.W.); (S.H.); (H.S.); (A.N.)
| | - Alexander M. P. Byrne
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Pauline M. van Diemen
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Shelley Rhodes
- Bacteriology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK;
| | - Joe James
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Benjamin Mollett
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Vivien J. Coward
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Paul Skinner
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Caroline J. Warren
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Kevin R. Bewley
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, UK; (K.R.B.); (K.A.R.); (Y.H.); (M.W.C.)
| | - Samantha Watson
- Pathology and Animal Sciences Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (F.Z.X.L.); (S.W.); (S.H.); (H.S.); (A.N.)
| | - Shellene Hurley
- Pathology and Animal Sciences Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (F.Z.X.L.); (S.W.); (S.H.); (H.S.); (A.N.)
| | - Kathryn A. Ryan
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, UK; (K.R.B.); (K.A.R.); (Y.H.); (M.W.C.)
| | - Yper Hall
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, UK; (K.R.B.); (K.A.R.); (Y.H.); (M.W.C.)
| | - Hugh Simmons
- Pathology and Animal Sciences Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (F.Z.X.L.); (S.W.); (S.H.); (H.S.); (A.N.)
| | - Alejandro Núñez
- Pathology and Animal Sciences Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (F.Z.X.L.); (S.W.); (S.H.); (H.S.); (A.N.)
| | - Miles W. Carroll
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, UK; (K.R.B.); (K.A.R.); (Y.H.); (M.W.C.)
- Nuffield Department of Medicine, Oxford University, Oxford OX1 3SY, UK
| | - Ian H. Brown
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Sharon M. Brookes
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
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628
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A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein. Nat Commun 2021; 12:288. [PMID: 33436577 PMCID: PMC7803729 DOI: 10.1038/s41467-020-20602-5] [Citation(s) in RCA: 181] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/10/2020] [Indexed: 12/28/2022] Open
Abstract
Vaccines and therapeutics are urgently needed for the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we screen human monoclonal antibodies (mAb) targeting the receptor binding domain (RBD) of the viral spike protein via antibody library constructed from peripheral blood mononuclear cells of a convalescent patient. The CT-P59 mAb potently neutralizes SARS-CoV-2 isolates including the D614G variant without antibody-dependent enhancement effect. Complex crystal structure of CT-P59 Fab/RBD shows that CT-P59 blocks interaction regions of RBD for angiotensin converting enzyme 2 (ACE2) receptor with an orientation that is notably different from previously reported RBD-targeting mAbs. Furthermore, therapeutic effects of CT-P59 are evaluated in three animal models (ferret, hamster, and rhesus monkey), demonstrating a substantial reduction in viral titer along with alleviation of clinical symptoms. Therefore, CT-P59 may be a promising therapeutic candidate for COVID-19. Therapies and vaccines for COVID-19, caused by the SARS-CoV-2 viral pandemic, are urgently needed. Here the authors establish and screen an antibody library from a convalescent COVID-19 patient to isolate a neutralizing antibody with the ability to reduce viral titer and alleviate symptoms in ferret, hamster, and rhesus monkey infection models.
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629
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Development and structural basis of a two-MAb cocktail for treating SARS-CoV-2 infections. Nat Commun 2021; 12:264. [PMID: 33431876 PMCID: PMC7801428 DOI: 10.1038/s41467-020-20465-w] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/03/2020] [Indexed: 01/10/2023] Open
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Neutralizing antibodies against SARS-CoV-2 are an option for drug development for treating COVID-19. Here, we report the identification and characterization of two groups of mouse neutralizing monoclonal antibodies (MAbs) targeting the receptor-binding domain (RBD) on the SARS-CoV-2 spike (S) protein. MAbs 2H2 and 3C1, representing the two antibody groups, respectively, bind distinct epitopes and are compatible in formulating a noncompeting antibody cocktail. A humanized version of the 2H2/3C1 cocktail is found to potently neutralize authentic SARS-CoV-2 infection in vitro with half inhibitory concentration (IC50) of 12 ng/mL and effectively treat SARS-CoV-2-infected mice even when administered at as late as 24 h post-infection. We determine an ensemble of cryo-EM structures of 2H2 or 3C1 Fab in complex with the S trimer up to 3.8 Å resolution, revealing the conformational space of the antigen–antibody complexes and MAb-triggered stepwise allosteric rearrangements of the S trimer, delineating a previously uncharacterized dynamic process of coordinated binding of neutralizing antibodies to the trimeric S protein. Our findings provide important information for the development of MAb-based drugs for preventing and treating SARS-CoV-2 infections. Here, the authors identify and characterize two mouse-derived monoclonal antibodies against SARS-CoV-2 spike protein that target different epitopes in RBD and block the interaction S/ACE2 and show that a formulated humanized version cocktail exhibits prophylaxis and therapeutic antiviral effects in an hACE2-adenovector expressed mouse model.
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630
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Insights from genomes and genetic epidemiology of SARS-CoV-2 isolates from the state of Andhra Pradesh. Epidemiol Infect 2021. [PMCID: PMC8367868 DOI: 10.1017/s0950268821001424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) emerged from a city in China and has now spread as a global pandemic affecting millions of individuals. The causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is being extensively studied in terms of its genetic epidemiology using genomic approaches. Andhra Pradesh is one of the major states of India with the third-largest number of COVID-19 cases with a limited understanding of its genetic epidemiology. In this study, we have sequenced 293 SARS-CoV-2 genome isolates from Andhra Pradesh with a mean coverage of 13324X. We identified 564 high-quality SARS-CoV-2 variants. A total of 18 variants mapped to reverse transcription polymerase chain reaction primer/probe sites, and four variants are known to be associated with an increase in infectivity. Phylogenetic analysis of the genomes revealed the circulating SARS-CoV-2 in Andhra Pradesh majorly clustered under the clade A2a (20A, 20B and 20C) (94%), whereas 6% fall under the I/A3i clade, a clade previously defined to be present in large numbers in India. To the best of our knowledge, this is the most comprehensive genetic epidemiological analysis performed for the state of Andhra Pradesh.
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631
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Srivastava S, Banu S, Singh P, Sowpati DT, Mishra RK. SARS-CoV-2 genomics: An Indian perspective on sequencing viral variants. J Biosci 2021; 46:22. [PMID: 33737495 PMCID: PMC7895735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 01/25/2021] [Indexed: 04/01/2024]
Abstract
Since its emergence as a pneumonia-like outbreak in the Chinese city of Wuhan in late 2019, the novel coronavirus disease COVID-19 has spread widely to become a global pandemic. The first case of COVID-19 in India was reported on 30 January 2020 and since then it has affected more than ten million people and resulted in around 150,000 deaths in the country. Over time, the viral genome has accumulated mutations as it passes through its human hosts, a common evolutionary mechanism found in all microorganisms. This has implications for disease surveillance and management, vaccines and therapeutics, and the emergence of reinfections. Sequencing the viral genome can help monitor these changes and provides an extraordinary opportunity to understand the genetic epidemiology and evolution of the virus as well as tracking its spread in a population. Here we review the past year in the context of the phylogenetic analysis of variants isolated over the course of the pandemic in India and highlight the importance of continued sequencing-based surveillance in the country.
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Affiliation(s)
- Surabhi Srivastava
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500 007 India
| | - Sofia Banu
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500 007 India
| | - Priya Singh
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500 007 India
| | - Divya Tej Sowpati
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500 007 India
| | - Rakesh K. Mishra
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500 007 India
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632
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Deb B, Vilvadrinath R, Goel S. COVID-19 variants that escape vaccine immunity: Global and Indian context-are more vaccines needed? J Biosci 2021; 46:112. [PMID: 34857677 PMCID: PMC8633907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/28/2021] [Indexed: 04/05/2024]
Abstract
The COVID-19 pandemic that emerged around December 2019 claimed millions of lives. For vaccine development, S protein on viral envelope that binds to ACE2 receptor on cells for entry was identified as vaccine candidate. S protein consists of Receptor Binding Motif (RBM) in the S1 subunit followed by the S2 subunit with an intermediate furin cleavage site. A stabilized version of S protein with 2 proline residues was used as antigen. Overall, most vaccines exhibited efficacy between 80 and 95%. However, being a RNA virus that is prone to mutations along with selection pressure on S protein and frequent use of convalescent plasma led to evolution of variants. These variants are responsible for multiple waves of infection observed globally. In our review, we discuss current data on vaccines and its efficacy in neutralizing SARS-CoV-2 from Wuhan and its variants. Further, our docked mutations observed in variants on the ACE2-S complex cryo-EM structure show that mostly the S1 domain is under selection pressure where major mutations occur in the N terminal domain (NTD), RBM and junction near S1-S2 subunit. Therefore, this review would be a reference for development of new candidate antigen(s) with better efficacy against variants.
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Affiliation(s)
- Bijayeeta Deb
- Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India
| | - Ramya Vilvadrinath
- Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India
| | - Suchi Goel
- Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India
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633
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Bayarri-Olmos R, Rosbjerg A, Johnsen LB, Helgstrand C, Bak-Thomsen T, Garred P, Skjoedt MO. The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. J Biol Chem 2021; 296:100536. [PMID: 33716040 PMCID: PMC7948531 DOI: 10.1016/j.jbc.2021.100536] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/02/2021] [Accepted: 03/09/2021] [Indexed: 12/18/2022] Open
Abstract
Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 from humans to animals has been reported for many domesticated species, including farmed minks. The identification of novel spike gene mutations appearing in minks has raised major concerns about potential immune evasion and challenges for the global vaccine strategy. One genetic variant, known as "cluster five," arose among farmed minks in Denmark and resulted in a complete shutdown of the world's largest mink production. However, the functional properties of this new variant are not established. Here we present functional data on the cluster-five variant, which contains a mutation resulting in a Y453F residue change in the receptor-binding domain (RBD) of the spike protein. Using an ELISA-based angiotensin-converting enzyme-2/RBD inhibition assay, we show that the Y453F variant does not decrease established humoral immunity from previously infected individuals or affect the neutralizing antibody response in a vaccine mouse model based on the original Wuhan strain RBD or spike as antigens. However, biolayer interferometry analysis demonstrates that it binds the human angiotensin-converting enzyme-2 receptor with a 4-fold higher affinity than the original strain, suggesting an enhanced transmission capacity and a possible challenge for viral control. These results also indicate that the rise in the frequency of the cluster-five variant in mink farms might be a result of the fitness advantage conferred by the receptor adaptation rather than evading immune responses.
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MESH Headings
- Amino Acid Substitution
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/immunology
- Animals
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/metabolism
- Antibodies, Viral/chemistry
- Antibodies, Viral/metabolism
- COVID-19/epidemiology
- COVID-19/immunology
- COVID-19/transmission
- Convalescence
- Denmark/epidemiology
- Gene Expression
- HEK293 Cells
- Host-Pathogen Interactions/genetics
- Host-Pathogen Interactions/immunology
- Humans
- Immune Sera/chemistry
- Immunity, Innate
- Mink/virology
- Models, Molecular
- Mutation
- Pandemics
- Protein Binding
- Protein Structure, Secondary
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Virus Internalization
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Affiliation(s)
- Rafael Bayarri-Olmos
- Laboratory of Molecular Medicine, Department of Clinical Immunology, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Anne Rosbjerg
- Laboratory of Molecular Medicine, Department of Clinical Immunology, University Hospital of Copenhagen, Copenhagen, Denmark; Institute of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Peter Garred
- Laboratory of Molecular Medicine, Department of Clinical Immunology, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Mikkel-Ole Skjoedt
- Laboratory of Molecular Medicine, Department of Clinical Immunology, University Hospital of Copenhagen, Copenhagen, Denmark; Institute of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.
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634
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Nidom RV, Indrasari S, Normalina I, Nidom AN, Afifah B, Dewi L, Putra AK, Ansori ANM, Kusala MKJ, Alamudi MY, Nidom CA. Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021. BULLETIN OF THE NATIONAL RESEARCH CENTRE 2021; 45:200. [PMID: 34840498 PMCID: PMC8606223 DOI: 10.1186/s42269-021-00657-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 11/07/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND Indonesia has started the big project of COVID-19 vaccination program since 13 January 2021 by employing the first shot of vaccine to the President of Indonesia as the outbreak and rapid transmission of COVID-19 have endangered not only Indonesian but the global health and economy. This study aimed to investigate the full-length genome mutation analysis of 166 Indonesian SARS-CoV-2 isolates as of 12 January 2021. RESULTS All data of the isolates were extracted from the Global Initiative on Sharing All Influenza Data (GISAID) EpiCoV database. CoVsurver platform was employed to investigate the full-length genome mutation analysis of all isolates. This study also focused on the phylogeny analysis in unlocking the mutation of S protein in Indonesian SARS-CoV-2 isolates. WIV04 isolate that was originated from Wuhan, China was used as the virus reference according to the CoVsurver default. The result showed that a full-length genome mutation analysis of 166 Indonesian SARS-CoV-2 isolates was successfully generated. Every single mutation in S protein was described and then visualized by utilizing BioRender platform. Furthermore, it also found that D614G mutation appeared in 103 Indonesian SARS-CoV-2 isolates. CONCLUSIONS To sum up, this study helped to observe the spread of COVID-19 transmission. However, it also proposed that the epidemiological surveillance and genomics studies might be improved on COVID-19 pandemic in Indonesia. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s42269-021-00657-0.
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Affiliation(s)
- Reviany V. Nidom
- Coronavirus and Vaccine Formulation Research Group, Professor Nidom Foundation, Surabaya, Indonesia
- Riset AIRC Indonesia, Surabaya, Indonesia
| | - Setyarina Indrasari
- Coronavirus and Vaccine Formulation Research Group, Professor Nidom Foundation, Surabaya, Indonesia
- Riset AIRC Indonesia, Surabaya, Indonesia
| | - Irine Normalina
- Coronavirus and Vaccine Formulation Research Group, Professor Nidom Foundation, Surabaya, Indonesia
- Riset AIRC Indonesia, Surabaya, Indonesia
| | - Astria N. Nidom
- Coronavirus and Vaccine Formulation Research Group, Professor Nidom Foundation, Surabaya, Indonesia
| | - Balqis Afifah
- Coronavirus and Vaccine Formulation Research Group, Professor Nidom Foundation, Surabaya, Indonesia
| | - Lestari Dewi
- Faculty of Medicine, Universitas Hang Tuah, Surabaya, Indonesia
| | | | - Arif N. M. Ansori
- Coronavirus and Vaccine Formulation Research Group, Professor Nidom Foundation, Surabaya, Indonesia
- Program Pendidikan Magister Menuju Doktor Untuk Sarjana Unggul (PMDSU) Program - Batch III, Ministry of Education, Culture, Research, and Technology, Jakarta, Indonesia
| | - Muhammad K. J. Kusala
- Coronavirus and Vaccine Formulation Research Group, Professor Nidom Foundation, Surabaya, Indonesia
- Program Pendidikan Magister Menuju Doktor Untuk Sarjana Unggul (PMDSU) Program - Batch III, Ministry of Education, Culture, Research, and Technology, Jakarta, Indonesia
| | - Mohammad Y. Alamudi
- Coronavirus and Vaccine Formulation Research Group, Professor Nidom Foundation, Surabaya, Indonesia
| | - Chairul A. Nidom
- Coronavirus and Vaccine Formulation Research Group, Professor Nidom Foundation, Surabaya, Indonesia
- Riset AIRC Indonesia, Surabaya, Indonesia
- Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia
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635
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Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. Genes (Basel) 2020; 12:genes12010016. [PMID: 33374416 PMCID: PMC7824201 DOI: 10.3390/genes12010016] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/11/2020] [Accepted: 12/22/2020] [Indexed: 12/15/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) glycoprotein D614G mutation became the predominant globally circulating variant after its emergence in the early coronavirus disease 2019 (COVID-19) pandemic. Studies showed that this mutation results in an open conformation of the S glycoprotein receptor-binding domain (RBD), and increased angiotensin 1-converting enzyme 2 (ACE2) binding and fusion, which result in an increase in SARS-CoV-2 transmissibility and infectivity. Dynamic tracking of SARS-CoV-2 showed that the D614G variant became predominant after emergence in Europe and North America, but not in China. The current absence of selective pressures from antiviral treatment suggests that the driving force for viral evolution could be variations in human population genetics. Results show that ACE2 expression is higher in Asian populations than that in European, North American, and African populations. This supports the idea that lower ACE2 expression is a driving force in the positive selection for the D614G mutation. This study suggests that the dynamics of the SARS-CoV-2 D614G mutation during the early-to-mid pandemic is associated with enhanced transmission efficiency in populations with lower ACE2 expression. Understanding the role that human genetic diversity plays in the adaptive evolution of SARS-CoV-2 may have an important impact on public health and measures to control the pandemic.
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636
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Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand. Nat Commun 2020; 11:6351. [PMID: 33311501 PMCID: PMC7733492 DOI: 10.1038/s41467-020-20235-8] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/19/2020] [Indexed: 01/12/2023] Open
Abstract
New Zealand, a geographically remote Pacific island with easily sealable borders, implemented a nationwide ‘lockdown’ of all non-essential services to curb the spread of COVID-19. Here, we generate 649 SARS-CoV-2 genome sequences from infected patients in New Zealand with samples collected during the ‘first wave’, representing 56% of all confirmed cases in this time period. Despite its remoteness, the viruses imported into New Zealand represented nearly all of the genomic diversity sequenced from the global virus population. These data helped to quantify the effectiveness of public health interventions. For example, the effective reproductive number, Re of New Zealand’s largest cluster decreased from 7 to 0.2 within the first week of lockdown. Similarly, only 19% of virus introductions into New Zealand resulted in ongoing transmission of more than one additional case. Overall, these results demonstrate the utility of genomic pathogen surveillance to inform public health and disease mitigation. New Zealand implemented stringent COVID-19 control measures early after identification of its first case. Here, the authors perform whole genome sequencing of samples taken until 22 May 2020 and find high viral diversity indicative of multiple separate introductions and limited community transmission.
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637
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Teng X, Li Q, Li Z, Zhang Y, Niu G, Xiao J, Yu J, Zhang Z, Song S. Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades. GENOMICS, PROTEOMICS & BIOINFORMATICS 2020; 18:648-663. [PMID: 33581339 PMCID: PMC7875716 DOI: 10.1016/j.gpb.2020.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/18/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023]
Abstract
COVID-19 and its causative pathogen SARS-CoV-2 have rushed the world into a staggering pandemic in a few months, and a global fight against both has been intensifying. Here, we describe an analysis procedure where genome composition and its variables are related, through the genetic code to molecular mechanisms, based on understanding of RNA replication and its feedback loop from mutation to viral proteome sequence fraternity including effective sites on the replicase-transcriptase complex. Our analysis starts with primary sequence information, identity-based phylogeny based on 22,051 SARS-CoV-2 sequences, and evaluation of sequence variation patterns as mutation spectra and its 12 permutations among organized clades. All are tailored to two key mechanisms: strand-biased and function-associated mutations. Our findings are listed as follows: 1) The most dominant mutation is C-to-U permutation, whose abundant second-codon-position counts alter amino acid composition toward higher molecular weight and lower hydrophobicity, albeit assumed most slightly deleterious. 2) The second abundance group includes three negative-strand mutations (U-to-C, A-to-G, and G-to-A) and a positive-strand mutation (G-to-U) due to DNA repair mechanisms after cellular abasic events. 3) A clade-associated biased mutation trend is found attributable to elevated level of negative-sense strand synthesis. 4) Within-clade permutation variation is very informative for associating non-synonymous mutations and viral proteome changes. These findings demand a platform where emerging mutations are mapped onto mostly subtle but fast-adjusting viral proteomes and transcriptomes, to provide biological and clinical information after logical convergence for effective pharmaceutical and diagnostic applications. Such actions are in desperate need, especially in the middle of the War against COVID-19.
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Affiliation(s)
- Xufei Teng
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianpeng Li
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhao Li
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuansheng Zhang
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangyi Niu
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingfa Xiao
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Yu
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhang Zhang
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shuhui Song
- China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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638
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Park HB, Lim SM, Hwang J, Zhang W, You S, Jin JO. Cancer immunotherapy using a polysaccharide from Codium fragile in a murine model. Oncoimmunology 2020; 9:1772663. [PMID: 32923129 PMCID: PMC7458636 DOI: 10.1080/2162402x.2020.1772663] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Natural polysaccharides have shown immune modulatory effects with low toxicity in both animal and human models. A previous study has shown that the polysaccharide from Codium fragile (CFP) promotes natural killer (NK) cell activation in mice. Since NK cell activation is mediated by dendritic cells (DCs), we examined the effect of CFP on DC activation and evaluated the subsequent induction of anti-cancer immunity in a murine model. Treatment with CFP induced activation of bone marrow-derived dendritic cells (BMDCs). Moreover, subcutaneous injection of CFP promoted the activation of spleen and lymph node DCs in vivo. CFP also induced activation of DCs in tumor-bearing mice, and combination treatment with CFP and ovalbumin (OVA) promoted OVA-specific T cell activation, which consequently promoted infiltration of IFN-γ-and TNF-α-producing OT-1 and OT-II cells into the tumors. Moreover, combination treatment using CFP and cancer self-antigen efficiently inhibited B16 tumor growth in the mouse model. Treatment with CFP also enhanced anti-PD-L1 antibody mediated anti-cancer immunity in the CT-26 carcinoma-bearing BALB/c mice. Taken together these data suggest that CFP may function as an adjuvant in the treatment of cancer by enhancing immune activation. Abbreviations CFP: Codium fragile polysaccharide; NK: natural killer; IFN: interferon; TNF: tumor necrosis factor; IL: interleukin; tdLN: tumor draining lymph node; BMDC: bone marrow-derived dendritic cell; OVA: ovalbumin; Ab: antibody; Ag: antigen; DC: dendritic cell; CTL: cytotoxic T lymphocyte; APC: antigen-presenting cell; pDC: plasmacytoid dendritic cell; mDC: myeloid dendritic cell; MHC: major histocompatibility complex; CR3: complement receptor type 3; TLR: Toll-like receptor; LPS: lipopolysaccharide; SP: sulfated polysaccharide; TRP2: tyrosinase-related protein 2; SR-A: scavenger receptor-A
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Affiliation(s)
- Hae-Bin Park
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Seong-Min Lim
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Juyoung Hwang
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Wei Zhang
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - SangGuan You
- Department of Marine Food Science and Technology, Gangneung-Wonju National University, Gangneung, South Korea
| | - Jun-O Jin
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
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