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Focosi D, Franchini M, Maggi F, Shoham S. COVID-19 therapeutics. Clin Microbiol Rev 2024; 37:e0011923. [PMID: 38771027 PMCID: PMC11237566 DOI: 10.1128/cmr.00119-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
SUMMARYSince the emergence of COVID-19 in 2020, an unprecedented range of therapeutic options has been studied and deployed. Healthcare providers have multiple treatment approaches to choose from, but efficacy of those approaches often remains controversial or compromised by viral evolution. Uncertainties still persist regarding the best therapies for high-risk patients, and the drug pipeline is suffering fatigue and shortage of funding. In this article, we review the antiviral activity, mechanism of action, pharmacokinetics, and safety of COVID-19 antiviral therapies. Additionally, we summarize the evidence from randomized controlled trials on efficacy and safety of the various COVID-19 antivirals and discuss unmet needs which should be addressed.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Massimo Franchini
- Division of Hematology and Transfusion Medicine, Carlo Poma Hospital, Mantua, Italy
| | - Fabrizio Maggi
- National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS, Rome, Italy
| | - Shmuel Shoham
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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2
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Willett JDS, Gravel A, Dubuc I, Gudimard L, Dos Santos Pereira Andrade AC, Lacasse É, Fortin P, Liu JL, Cervantes JA, Galvez JH, Djambazian HHV, Zwaig M, Roy AM, Lee S, Chen SH, Ragoussis J, Flamand L. SARS-CoV-2 rapidly evolves lineage-specific phenotypic differences when passaged repeatedly in immune-naïve mice. Commun Biol 2024; 7:191. [PMID: 38365933 PMCID: PMC10873417 DOI: 10.1038/s42003-024-05878-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 02/01/2024] [Indexed: 02/18/2024] Open
Abstract
The persistence of SARS-CoV-2 despite the development of vaccines and a degree of herd immunity is partly due to viral evolution reducing vaccine and treatment efficacy. Serial infections of wild-type (WT) SARS-CoV-2 in Balb/c mice yield mouse-adapted strains with greater infectivity and mortality. We investigate if passaging unmodified B.1.351 (Beta) and B.1.617.2 (Delta) 20 times in K18-ACE2 mice, expressing the human ACE2 receptor, in a BSL-3 laboratory without selective pressures, drives human health-relevant evolution and if evolution is lineage-dependent. Late-passage virus causes more severe disease, at organism and lung tissue scales, with late-passage Delta demonstrating antibody resistance and interferon suppression. This resistance co-occurs with a de novo spike S371F mutation, linked with both traits. S371F, an Omicron-characteristic mutation, is co-inherited at times with spike E1182G per Nanopore sequencing, existing in different within-sample viral variants at others. Both S371F and E1182G are linked to mammalian GOLGA7 and ZDHHC5 interactions, which mediate viral-cell entry and antiviral response. This study demonstrates SARS-CoV-2's tendency to evolve with phenotypic consequences, its evolution varying by lineage, and suggests non-dominant quasi-species contribution.
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Affiliation(s)
- Julian Daniel Sunday Willett
- Quantitative Life Sciences Ph.D. Program, McGill University, Montreal, QC, Canada
- McGill Genome Centre, McGill University, Montreal, QC, Canada
- Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Annie Gravel
- Axe maladies infectieuses et immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec, Canada
| | - Isabelle Dubuc
- Axe maladies infectieuses et immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec, Canada
| | - Leslie Gudimard
- Axe maladies infectieuses et immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec, Canada
| | | | - Émile Lacasse
- Axe maladies infectieuses et immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec, Canada
| | - Paul Fortin
- Axe maladies infectieuses et immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec, Canada
- Centre de Recherche ARThrite-Arthrite, Recherche et Traitements, Université Laval, Québec, QC, Canada
- Division of Rheumatology, Department of Medicine, CHU de Québec-Université Laval, Québec, QC, Canada
| | - Ju-Ling Liu
- McGill Genome Centre, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Jose Avila Cervantes
- McGill Genome Centre, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Jose Hector Galvez
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada
| | - Haig Hugo Vrej Djambazian
- McGill Genome Centre, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Melissa Zwaig
- McGill Genome Centre, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Anne-Marie Roy
- McGill Genome Centre, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Sally Lee
- McGill Genome Centre, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Shu-Huang Chen
- McGill Genome Centre, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Jiannis Ragoussis
- McGill Genome Centre, McGill University, Montreal, QC, Canada.
- Department of Human Genetics, McGill University, Montreal, QC, Canada.
| | - Louis Flamand
- Axe maladies infectieuses et immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec, Canada.
- Département de microbiologie-infectiologie et d'immunologie, Université Laval, Québec, QC, Canada.
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Focosi D, McConnell S, Sullivan DJ, Casadevall A. Analysis of SARS-CoV-2 mutations associated with resistance to therapeutic monoclonal antibodies that emerge after treatment. Drug Resist Updat 2023; 71:100991. [PMID: 37572569 DOI: 10.1016/j.drup.2023.100991] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/18/2023] [Accepted: 07/30/2023] [Indexed: 08/14/2023]
Abstract
The mutation rate of the Omicron sublineage has led to baseline resistance against all previously authorized anti-Spike monoclonal antibodies (mAbs). Nevertheless, in case more antiviral mAbs will be authorized in the future, it is relevant to understand how frequently treatment-emergent resistance has emerged so far, under different combinations and in different patient subgroups. We report the results of a systematic review of the medical literature for case reports and case series for treatment-emergent immune escape, which is defined as emergence of a resistance-driving mutation in at least 20% of sequences in a given host at a given timepoint. We identified 32 publications detailing 216 cases that included different variants of concern (VOC) and found that the incidence of treatment emergent-resistance ranged from 10% to 50%. Most of the treatment-emergent resistance events occurred in immunocompromised patients. Interestingly, resistance also emerged against cocktails of two mAbs, albeit at lower frequencies. The heterogenous therapeutic management of those cases doesn't allow inferences about the clinical outcome in patients with treatment-emergent resistance. Furthermore, we noted a temporal correlation between the introduction of mAb therapies and a subsequent increase in SARS-CoV-2 sequences across the globe carrying mutations conferring resistance to that mAb, raising concern as to whether these had originated in mAb-treated individuals. Our findings confirm that treatment-emergent immune escape to anti-Spike mAbs represents a frequent and concerning phenomenon and suggests that these are associated with mAb use in immunosuppressed hosts.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Italy.
| | - Scott McConnell
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - David J Sullivan
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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4
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Abduljaleel Z, Melebari S, Athar M, Dehlawi S, Udhaya Kumar S, Aziz SA, Dannoun AI, Malik SM, Thasleem J, George Priya Doss C. SARS-CoV-2 vaccine breakthrough infections (VBI) by Omicron variant (B.1.1.529) and consequences in structural and functional impact. Cell Signal 2023:110798. [PMID: 37423342 DOI: 10.1016/j.cellsig.2023.110798] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/18/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023]
Abstract
This study investigated the efficacy of existing vaccines against hospitalization and infection due to the Omicron variant of COVID-19, particularly for those who received two doses of Moderna or Pfizer vaccines and one dose of Johnson & Johnson vaccine or who were vaccinated more than five months before. A total of 36 variants in Omicron's spike protein, targeted by all three vaccinations, have made antibodies less effective at neutralizing the virus. The genotyping of the SARS-CoV-2 viral sequence revealed clinically significant variants such as E484K in three genetic mutations (T95I, D614G, and del142-144). A woman showed two of these mutations, indicating a potential risk of infection after successful immunization, as recently reported by Hacisuleyman (2021). We examine the effects of mutations on domains (NID, RBM, and SD2) found at the interfaces of the spike domains Omicron B.1.1529, Delta/B.1.1529, Alpha/B.1.1.7, VUM B.1.526, B.1.575.2, and B.1.1214 (formerly VOI Iota). We tested the affinity of Omicron for ACE2 and found that the wild- and mutant-spike proteins were using atomistic molecular dynamics simulations. According to the binding free energies calculated during mutagenesis, the ACE2 bound Omicron spikes more strongly than the wild strain SARS-CoV-2. T95I, D614G, and E484K are three substitutions that significantly contribute to RBD, corresponding to ACE2 binding energies and a doubling of the electrostatic potential of Omicron spike proteins. The Omicron appears to bind to ACE2 with greater affinity, increasing its infectivity and transmissibility. The spike virus was designed to strengthen antibody immune evasion through binding while boosting receptor binding by enhancing IgG and IgM antibodies that stimulate human β-cell, as opposed to the wild strain, which has more vital stimulation of both antibodies.
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Affiliation(s)
- Zainularifeen Abduljaleel
- Science and Technology Unit, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia; Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia.
| | - Sami Melebari
- Department of Molecular Biology, The Regional Laboratory, Ministry of Health (MOH), Makkah, Saudi Arabia
| | - Mohammed Athar
- Science and Technology Unit, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia; Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia
| | - Saied Dehlawi
- Department of Molecular Biology, The Regional Laboratory, Ministry of Health (MOH), Makkah, Saudi Arabia
| | - S Udhaya Kumar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Syed A Aziz
- Department of Pathology and Lab Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Anas Ibrahim Dannoun
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia
| | - Shaheer M Malik
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Jasheela Thasleem
- Jamal Mohamed College, Bharathidasan University, 7, Race Course Road, Kaja Nagar, Tiruchirappalli, Tamil Nadu 620020, India
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
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5
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Li F, Xu W, Zhang X, Wang W, Su S, Han P, Wang H, Xu Y, Li M, Fan L, Zhang H, Dai Q, Lin H, Qi X, Liang J, Wang X, Jiang S, Xie Y, Lu L, Yang X. A spike-targeting bispecific T cell engager strategy provides dual layer protection against SARS-CoV-2 infection in vivo. Commun Biol 2023; 6:592. [PMID: 37264086 DOI: 10.1038/s42003-023-04955-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/18/2023] [Indexed: 06/03/2023] Open
Abstract
Neutralizing antibodies exert a potent inhibitory effect on viral entry; however, they are less effective in therapeutic models than in prophylactic models, presumably because of their limited efficacy in eliminating virus-producing cells via Fc-mediated cytotoxicity. Herein, we present a SARS-CoV-2 spike-targeting bispecific T-cell engager (S-BiTE) strategy for controlling SARS-CoV-2 infection. This approach blocks the entry of free virus into permissive cells by competing with membrane receptors and eliminates virus-infected cells via powerful T cell-mediated cytotoxicity. S-BiTE is effective against both the original and Delta variant of SARS-CoV2 with similar efficacy, suggesting its potential application against immune-escaping variants. In addition, in humanized mouse model with live SARS-COV-2 infection, S-BiTE treated mice showed significantly less viral load than neutralization only treated group. The S-BiTE strategy may have broad applications in combating other coronavirus infections.
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Affiliation(s)
- Fanlin Li
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences and Biosafety Level 3 Laboratory, Fudan University, Shanghai, 200032, China
| | - Xiaoqing Zhang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Physiology, Naval Medical University, Shanghai, 200433, China
| | - Wanting Wang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shan Su
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences and Biosafety Level 3 Laboratory, Fudan University, Shanghai, 200032, China
| | - Ping Han
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Haiyong Wang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yanqin Xu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Min Li
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lilv Fan
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Huihui Zhang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qiang Dai
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hao Lin
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xinyue Qi
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jie Liang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xin Wang
- Shanghai Longyao Biotechnology Limited, Shanghai, 201203, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences and Biosafety Level 3 Laboratory, Fudan University, Shanghai, 200032, China
| | - Youhua Xie
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences and Biosafety Level 3 Laboratory, Fudan University, Shanghai, 200032, China.
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences and Biosafety Level 3 Laboratory, Fudan University, Shanghai, 200032, China.
| | - Xuanming Yang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Riguero V, Delmar J, Dippel A, McTamney P, Luo E, Martinez A, Ren K, van Dyk N, O'Connor E. A scalable and high yielding SARS-CoV-2 spike protein receptor binding domain production process. Protein Expr Purif 2023; 205:106241. [PMID: 36736512 PMCID: PMC9890279 DOI: 10.1016/j.pep.2023.106241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 02/05/2023]
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spike protein is of interest for the development of vaccines and therapeutics against COVID-19. Vaccines are designed to raise an immune response against the spike protein. Other therapies attempt to block the interaction of the spike protein and mammalian cells. Therefore, the spike protein itself and specific interacting regions of the spike protein are reagents required by industry to enable the advancement of medicines to combat SARS-CoV-2. Early production methods of the SARS-CoV-2 spike protein receptor binding domain (RBD) were labor intensive with scalability challenges. In this work, we describe a high yielding and scalable production process for the SARS-CoV-2 RBD. Expression was performed in human embryonic kidney (HEK) 293 cells followed by a two-column purification process including immobilized metal affinity chromatography (IMAC) followed by Ceramic Hydroxyapatite (CHT). The improved process showed good scalability, enabling efficient purification of 2.5 g of product from a 200 L scale bioreactor.
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Affiliation(s)
- Valeria Riguero
- Purification Process Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Jared Delmar
- Analytical Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Andrew Dippel
- Biological Engineering, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Patrick McTamney
- Biological Engineering, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Ethan Luo
- Cell Culture and Fermentation Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Antonio Martinez
- Manufacturing Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Kuishu Ren
- Biological Engineering, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Nydia van Dyk
- Biological Engineering, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Ellen O'Connor
- Purification Process Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, 20878, USA. ellen.o'
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7
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Tada T, Dcosta BM, Zhou H, Landau NR. Prophylaxis and treatment of SARS-CoV-2 infection by an ACE2 receptor decoy in a preclinical animal model. iScience 2023; 26:106092. [PMID: 36741912 PMCID: PMC9886562 DOI: 10.1016/j.isci.2023.106092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/09/2022] [Accepted: 01/26/2023] [Indexed: 02/01/2023] Open
Abstract
The emergence of SARS-CoV-2 variants with highly mutated spike proteins has presented an obstacle to the use of monoclonal antibodies for the prevention and treatment of SARS-CoV-2 infection. We show that a high-affinity receptor decoy protein in which a modified ACE2 ectodomain is fused to a single domain of an immunoglobulin heavy chain Fc region dramatically suppressed virus loads in mice upon challenge with a high dose of parental SARS-CoV-2 or Omicron variants. The decoy also potently suppressed virus replication when administered shortly post-infection. The decoy approach offers protection against the current viral variants and, potentially, against SARS-CoV-2 variants that may emerge with the continued evolution of the spike protein or novel viruses that use ACE2 for virus entry.
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Affiliation(s)
- Takuya Tada
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, Rm 509, New York, NY 10016, USA
| | - Belinda M. Dcosta
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, Rm 509, New York, NY 10016, USA
| | - Hao Zhou
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, Rm 509, New York, NY 10016, USA
| | - Nathaniel R. Landau
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, Rm 509, New York, NY 10016, USA
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8
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Prophylaxis and Treatment of SARS-CoV-2 infection by an ACE2 Receptor Decoy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2022.12.31.522401. [PMID: 36656772 PMCID: PMC9844012 DOI: 10.1101/2022.12.31.522401] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The emergence of SARS-CoV-2 variants with highly mutated spike proteins has presented an obstacle to the use of monoclonal antibodies for the prevention and treatment of SARS-CoV-2 infection. We show that a high affinity receptor decoy protein in which a modified ACE2 ectodomain is fused to a single domain of an immunoglobulin heavy chain Fc region dramatically suppressed virus loads in mice upon challenge with a high dose of parental SARS-CoV-2 or Omicron variants. The decoy also potently suppressed virus replication when administered shortly post-infection. The decoy approach offers protection against the current viral variants and, potentially, against SARS-CoV-2 variants that may emerge with the continued evolution of the spike protein or novel viruses that use ACE2 for virus entry.
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9
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Wang Q, Peng L, Nie Y, Shu Y, Zhang H, Song Z, Li Y, Hu H, Li L, Wang X, Liu J, Li J, Shi Z, Deng F, Guo Y, Zhou Y, Yan B, Hu Z, Wang M. Hybridoma-derived neutralizing monoclonal antibodies against Beta and Delta variants of SARS-CoV-2 in vivo. Virol Sin 2022; 38:257-267. [PMID: 36596381 PMCID: PMC9803610 DOI: 10.1016/j.virs.2022.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023] Open
Abstract
Neutralizing monoclonal antibodies (mAb) are a major therapeutic strategy for the treatment of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. The continuous emergence of new SARS-CoV-2 variants worldwide has increased the urgency for the development of new mAbs. In this study, we immunized mice with the receptor-binding domain (RBD) of the SARS-CoV-2 prototypic strain (WIV04) and screened 35 RBD-specific mAbs using hybridoma technology. Results of the plaque reduction neutralization test showed that 25 of the mAbs neutralized authentic WIV04 strain infection. The 25 mAbs were divided into three categories based on the competitive enzyme-linked immunosorbent assay results. A representative mAb was selected from each category (RD4, RD10, and RD14) to determine the binding kinetics and median inhibitory concentration (IC50) of WIV04 and two variants of concern (VOC): B.1.351 (Beta) and B.1.617.2 (Delta). RD4 neutralized the B.1.617.2 variant with an IC50 of 2.67 ng/mL; however, it completely lost neutralizing activity against the B.1.351 variant. RD10 neutralized both variants with an IC50 exceeding 100 ng/mL; whereas RD14 neutralized two variants with a higher IC50 (>1 mg/mL). Animal experiments were performed to evaluate the protective effects of RD4 and RD10 against various VOC infections. RD4 could protect Adv-hACE2 transduced mice from B.1.617.2 infection at an antibody concentration of 25 mg/kg, while RD10 could protect mice from B.1.351 infection at an antibody concentration of 75 mg/kg. These results highlight the potential for future modifications of the mAbs for practical use.
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Affiliation(s)
- Qianran Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Lu Peng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yanqiu Nie
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yanni Shu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Huajun Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zidan Song
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yufeng Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hengrui Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Liushuai Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xi Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jia Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jiang Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zhengli Shi
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Fei Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yu Guo
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yiwu Zhou
- Department of Forensic Medicine, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, 430010, China
| | - Bing Yan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zhihong Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Manli Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China,Hubei Jiangxia Laboratory, Wuhan, 430200, China,Corresponding author
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10
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Christie SM, Tada T, Yin Y, Bhardwaj A, Landau NR, Rothenberg E. Single-virus tracking reveals variant SARS-CoV-2 spike proteins induce ACE2-independent membrane interactions. SCIENCE ADVANCES 2022; 8:eabo3977. [PMID: 36490345 PMCID: PMC9733935 DOI: 10.1126/sciadv.abo3977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) became a global health crisis after its emergence in 2019. Replication of the virus is initiated by binding of the viral spike (S) protein to human angiotensin-converting enzyme 2 (ACE2) on the target cell surface. Mutations acquired by SARS-CoV-2 S variants likely influence virus-target cell interaction. Here, using single-virus tracking to capture these initial steps, we observe how viruses carrying variant S interact with target cells. Specificity for ACE2 occurs for viruses with the reference sequence or D614G mutation. Analysis of the Alpha, Beta, and Delta SARS-CoV-2 variant S proteins revealed a progressive altered cell interaction with a reduced dependence on ACE2. Notably, the Delta variant S affinity was independent of ACE2. These enhanced interactions may account for the increased transmissibility of variants. Knowledge of how mutations influence cell interaction is essential for vaccine development against emerging variants of SARS-CoV-2.
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Affiliation(s)
- Shaun M. Christie
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Takuya Tada
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Yandong Yin
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Amit Bhardwaj
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Nathaniel R. Landau
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
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11
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Bian L, Liu J, Gao F, Gao Q, He Q, Mao Q, Wu X, Xu M, Liang Z. Research progress on vaccine efficacy against SARS-CoV-2 variants of concern. Hum Vaccin Immunother 2022; 18:2057161. [PMID: 35438600 PMCID: PMC9115786 DOI: 10.1080/21645515.2022.2057161] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 03/08/2022] [Accepted: 03/21/2022] [Indexed: 01/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate worldwide and a variety of variants have emerged. Variants of concern (VOC) designated by the World Health Organization (WHO) have triggered epidemic waves due to their strong infectivity or pathogenicity and potential immune escape, among other reasons. Although large-scale vaccination campaigns undertaken globally have contributed to the improved control of SARS-CoV-2, the efficacies of current vaccines against VOCs have declined to various degrees. In particular, the highly infectious Delta and Omicron variants have caused recent epidemics and prompted concerns about control measures. This review summarizes current VOCs, the protective efficacy of vaccines against VOCs, and the shortcomings in methods for evaluating vaccine efficacy. In addition, strategies for responding to variants are proposed for future epidemic prevention and control as well as for vaccine research and development.
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Affiliation(s)
- Lianlian Bian
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Jianyang Liu
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Fan Gao
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Qiushuang Gao
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Qian He
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Qunying Mao
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Xing Wu
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Miao Xu
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Zhenglun Liang
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
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12
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Mucosal immunization with a delta-inulin adjuvanted recombinant spike vaccine elicits lung-resident immune memory and protects mice against SARS-CoV-2. Mucosal Immunol 2022; 15:1405-1415. [PMID: 36411332 PMCID: PMC9676795 DOI: 10.1038/s41385-022-00578-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 09/12/2022] [Accepted: 10/09/2022] [Indexed: 11/22/2022]
Abstract
Multiple SARS-CoV-2 vaccine candidates have been approved for use and have had a major impact on the COVID-19 pandemic. There remains, however, a significant need for vaccines that are safe, easily transportable and protective against infection, as well as disease. Mucosal vaccination is favored for its ability to induce immune memory at the site of infection, making it appealing for SARS-CoV-2 vaccine strategies. In this study we performed in-depth analysis of the immune responses in mice to a subunit recombinant spike protein vaccine formulated with the delta-inulin adjuvant Advax when administered intratracheally (IT), versus intramuscular delivery (IM). Both routes produced robust neutralizing antibody titers (NAb) and generated sterilizing immunity against SARS-CoV-2. IT delivery, however, produced significantly higher systemic and lung-local NAb that resisted waning up to six months post vaccination, and only IT delivery generated inducible bronchus-associated lymphoid tissue (iBALT), a site of lymphocyte antigen presentation and proliferation. This was coupled with robust and long-lasting lung tissue-resident memory CD4+ and CD8+ T cells that were not observed in IM-vaccinated mice. This study provides a detailed view of the lung-resident cellular response to IT vaccination against SARS-CoV-2 and demonstrates the importance of delivery site selection in the development of vaccine candidates.
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13
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Delshad M, Sanaei MJ, Pourbagheri-Sigaroodi A, Bashash D. Host genetic diversity and genetic variations of SARS-CoV-2 in COVID-19 pathogenesis and the effectiveness of vaccination. Int Immunopharmacol 2022; 111:109128. [PMID: 35963158 PMCID: PMC9359488 DOI: 10.1016/j.intimp.2022.109128] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/15/2022] [Accepted: 08/03/2022] [Indexed: 12/14/2022]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for the outbreak of coronavirus disease 2019 (COVID-19), has shown a vast range of clinical manifestations from asymptomatic to life-threatening symptoms. To figure out the cause of this heterogeneity, studies demonstrated the trace of genetic diversities whether in the hosts or the virus itself. With this regard, this review provides a comprehensive overview of how host genetic such as those related to the entry of the virus, the immune-related genes, gender-related genes, disease-related genes, and also host epigenetic could influence the severity of COVID-19. Besides, the mutations in the genome of SARS-CoV-2 __leading to emerging of new variants__ per se affect the affinity of the virus to the host cells and enhance the immune escape capacity. The current review discusses these variants and also the latest data about vaccination effectiveness facing the most important variants.
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Affiliation(s)
- Mahda Delshad
- Department of Laboratory Sciences, School of Allied Medical Sciences, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mohammad-Javad Sanaei
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Atieh Pourbagheri-Sigaroodi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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14
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Alesci A, Gitto M, Kotańska M, Lo Cascio P, Miller A, Nicosia N, Fumia A, Pergolizzi S. Immunogenicity, effectiveness, safety and psychological impact of COVID-19 mRNA vaccines. Hum Immunol 2022; 83:755-767. [PMID: 35963787 PMCID: PMC9359511 DOI: 10.1016/j.humimm.2022.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 07/10/2022] [Accepted: 08/03/2022] [Indexed: 12/15/2022]
Abstract
In December 2019, a new single-stranded RNA coronavirus, SARS-CoV-2, appeared in China and quickly spread around the world leading to a pandemic. Infection with SARS-CoV-2 generates symptoms ranging from asymptomatic to severe, occasionally requiring hospitalization in intensive care units, and, in more severe cases, leading to death. Scientists and researchers around the world have made a real race against time to develop various vaccines to slow down and stop the spread of the virus. In addition to conventional viral vector vaccines, new generation mRNA vaccines, BNT152b2 (Comirnaty) and mRNA-1273 (Spikevax), have been developed respectively by Pfizer/BioNTech and Moderna. These vaccines act on immune cells to induce an immune response with the production of specific antibodies against Spike protein of SARS-CoV-2, and to stimulate the differentiation of T and B memory cells. The objective of this review is to provide a detailed picture of the validity of these new vaccines and the safety of vaccination. Not only was the immunogenic effect of mRNA vaccines evaluated, but also the psychosocial impact they had on the population. The data collected show that this type of vaccine can also be an excellent candidate for future treatment and eradication of possible new pathologies with viral and non-viral etiology.
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Affiliation(s)
- Alessio Alesci
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy.
| | - Marco Gitto
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy; Phoniatric Unit, Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, 20157 Milan, Italy.
| | - Magdalena Kotańska
- Department of Pharmacological Screening, Jagiellonian University, Medical College, PL 30-688 Cracow, Poland.
| | - Patrizia Lo Cascio
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy.
| | - Anthea Miller
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell'Annunziata, 98168 Messina, Italy.
| | - Noemi Nicosia
- Department of Pharmacological Screening, Jagiellonian University, Medical College, PL 30-688 Cracow, Poland; Division of Neuroscience, Vita Salute San Raffaele University, 20132, Milan, Italy.
| | - Angelo Fumia
- Department of Clinical and Experimental Medicine, University of Messina, Padiglione C, A. O. U. Policlinico "G. Martino", 98147 Messina, Italy.
| | - Simona Pergolizzi
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy.
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15
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Lin Y, Zhu J, Liu Z, Li C, Guo Y, Wang Y, Chen K. Kinetics of severe acute respiratory syndrome coronavirus 2 infection antibody responses. Front Immunol 2022; 13:864278. [PMID: 35990623 PMCID: PMC9389018 DOI: 10.3389/fimmu.2022.864278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread rapidly throughout the world, causing severe morbidity and mortality. Since the first reports of Coronavirus disease 2019 (COVID-19) in late 2019, research on the characteristics of specific humoral immunity against SARS-CoV-2 in patients with COVID-19 has made great progress. However, our knowledge of persistent humoral immunity to SARS-CoV-2 infection is limited. The existence of protective immunity after infection will affect future transmission and disease severity. Therefore, it is important to gather knowledge about the kinetics of antibody responses. In this review, we summarize the information obtained so far on the characteristics and kinetics of the SARS-CoV-2 infection of specific humoral immune response, especially in neutralizing antibodies and their relationship with disease severity. In addition, with the emergence of variants of concern, we summarize the neutralizing effect of specific humoral immunity on variants of concern after the initial SARS-CoV-2 infection and vaccination.
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Affiliation(s)
- Yajie Lin
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Jiajie Zhu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Zongming Liu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Chaonan Li
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Yikai Guo
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Ying Wang
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, Zhejiang Provincial Clinical Research Centre for Oral Diseases, Cancer Centre of Zhejiang University, Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Ying Wang, ; Keda Chen,
| | - Keda Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
- *Correspondence: Ying Wang, ; Keda Chen,
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16
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Ssenyange G, Kerfoot M, Zhao M, Farhadian S, Chen S, Peng L, Ren P, Dela Cruz CS, Gupta S, Sutton RE. Development of an efficient reproducible cell-cell transmission assay for rapid quantification of SARS-CoV-2 spike interaction with hACE2. CELL REPORTS METHODS 2022; 2:100252. [PMID: 35757815 PMCID: PMC9213030 DOI: 10.1016/j.crmeth.2022.100252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/28/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Efficient quantitative assays for measurement of viral replication and infectivity are indispensable for future endeavors to develop prophylactic or therapeutic antiviral drugs or vaccines against SARS-CoV-2. We developed a SARS-CoV-2 cell-cell transmission assay that provides a rapid and quantitative readout to assess SARS-CoV-2 spike hACE2 interaction in the absence of pseudotyped particles or live virus. We established two well-behaved stable cell lines, which demonstrated a remarkable correlation with standard cell-free viral pseudotyping for inhibition by convalescent sera, small-molecule drugs, and murine anti-spike monoclonal antibodies. The assay is rapid, reliable, and highly reproducible, without a requirement for any specialized research reagents or laboratory equipment and should be easy to adapt for use in most investigative and clinical settings. It can be effectively used or modified for high-throughput screening for compounds and biologics that interfere with virus-cell binding and entry to complement other neutralization assays currently in use.
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Affiliation(s)
- George Ssenyange
- Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06510, USA
| | - Maya Kerfoot
- Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06510, USA
| | - Min Zhao
- Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06510, USA
| | - Shelli Farhadian
- Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sidi Chen
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Lei Peng
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Ping Ren
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Charles S. Dela Cruz
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Shaili Gupta
- Department of Medicine, Section of General Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Medicine, Veterans Affairs Healthcare Systems of Connecticut, West Haven, CT 06516, USA
| | - Richard E. Sutton
- Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Medicine, Veterans Affairs Healthcare Systems of Connecticut, West Haven, CT 06516, USA
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17
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Comparative analysis of human immune responses following SARS-CoV-2 vaccination with BNT162b2, mRNA-1273, or Ad26.COV2.S. NPJ Vaccines 2022; 7:77. [PMID: 35794181 PMCID: PMC9258461 DOI: 10.1038/s41541-022-00504-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 06/22/2022] [Indexed: 12/30/2022] Open
Abstract
SARS-CoV-2 vaccines BNT162b2, mRNA-1273, and Ad26.COV2.S received emergency use authorization by the U.S. Food and Drug Administration in 2020/2021. Individuals being vaccinated were invited to participate in a prospective longitudinal comparative study of immune responses elicited by the three vaccines. In this observational cohort study, immune responses were evaluated using a SARS-CoV-2 spike protein receptor-binding domain ELISA, SARS-CoV-2 virus neutralization assays and an IFN- γ ELISPOT assay at various times over six months following initial vaccination. mRNA-based vaccines elicited higher magnitude humoral responses than Ad26.COV2.S; mRNA-1273 elicited the most durable humoral response, and all humoral responses waned over time. Neutralizing antibodies against the Delta variant were of lower magnitude than the wild-type strain for all three vaccines. mRNA-1273 initially elicited the greatest magnitude of T cell response, but this declined by 6 months. Declining immunity over time supports the use of booster dosing, especially in the setting of emerging variants.
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18
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Muecksch F, Wise H, Templeton K, Batchelor B, Squires M, McCance K, Jarvis L, Malloy K, Furrie E, Richardson C, MacGuire J, Godber I, Burns A, Mavin S, Zhang F, Schmidt F, Bieniasz PD, Jenks S, Hatziioannou T. Longitudinal variation in SARS-CoV-2 antibody levels and emergence of viral variants: a serological analysis. THE LANCET. MICROBE 2022; 3:e493-e502. [PMID: 35636436 PMCID: PMC9141682 DOI: 10.1016/s2666-5247(22)00090-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 03/14/2022] [Accepted: 03/28/2022] [Indexed: 12/20/2022]
Abstract
BACKGROUND Serological assays are being used to monitor antibody responses in individuals who had SARS-CoV-2 infection and those who received a COVID-19 vaccine. We aimed to determine whether such assays can predict neutralising antibody titres as antibody levels wane and viral variants emerge. METHODS We measured antibody levels in serum samples from a cohort of 112 participants with SARS-CoV-2 infection using ten high-throughput serological tests and functional neutralisation assays. Serum samples were taken at baseline and at up to four subsequent visits. We assessed the effects of time and spike protein sequence variation on the performance and predictive value of the various assays. We did correlation analyses for individual timepoints using non-parametric Spearman correlation, and differences between timepoints were determined by use of a two-tailed Wilcoxon matched-pairs signed rank test. FINDINGS Neutralising antibody titres decreased over the first few months post-infection but stabilised thereafter, at about 30% of the level observed shortly after infection. Serological assays commonly used to measure antibodies against SARS-CoV-2 displayed a range of sensitivities that declined to varying extents over time. Quantitative measurements generated by serological assays based on the spike protein were better at predicting neutralising antibody titres than those based on nucleocapsid, but performance was variable, and manufacturer positivity thresholds were not able to predict the presence or absence of detectable neutralising activity. Although we observed some deterioration in correlation between serological measurements and functional neutralisation activity, some assays maintained an ability to predict neutralising titres, even against variants of concern. INTERPRETATION The ability of high-throughput serological assays to predict neutralising antibody titres is likely to be crucial for evaluation of immunity at the population scale. These data can facilitate the selection of the most suitable assays as surrogates of functional neutralising activity and suggest that such measurements might be useful in clinical practice. FUNDING US National Institutes of Health and National Health Service Research Scotland BioResource.
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Affiliation(s)
- Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Helen Wise
- Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK
| | - Kate Templeton
- Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK
| | - Becky Batchelor
- Department of Blood Sciences, Western General Hospital, Edinburgh, UK
| | - Maria Squires
- Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK
| | - Kirsty McCance
- Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK
| | - Lisa Jarvis
- SNBTS Microbiology Reference Laboratory, The Jack Copland Centre, Edinburgh, UK
| | - Kristen Malloy
- SNBTS Microbiology Reference Laboratory, The Jack Copland Centre, Edinburgh, UK
| | - Elizabeth Furrie
- Department of Immunology, Ninewells Hospital and Medical School, NHS Tayside, Dundee, UK
| | - Claire Richardson
- Department of Biochemistry, University Hospital Monklands, NHS Lanarkshire, Airdrie, UK
| | - Jacqueline MacGuire
- Department of Biochemistry, University Hospital Monklands, NHS Lanarkshire, Airdrie, UK
| | - Ian Godber
- Department of Biochemistry, Queen Elizabeth University Hospital, Glasgow, UK
| | - Alana Burns
- Department of Biochemistry, Queen Elizabeth University Hospital, Glasgow, UK
| | - Sally Mavin
- Scottish Microbiology Reference Laboratory, NHS Highland, Inverness, UK
| | - Fengwen Zhang
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Sara Jenks
- Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK.
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19
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Sun C, Xie C, Bu GL, Zhong LY, Zeng MS. Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants. Signal Transduct Target Ther 2022; 7:202. [PMID: 35764603 PMCID: PMC9240077 DOI: 10.1038/s41392-022-01039-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/16/2022] [Accepted: 05/22/2022] [Indexed: 01/18/2023] Open
Abstract
The persistent COVID-19 pandemic since 2020 has brought an enormous public health burden to the global society and is accompanied by various evolution of the virus genome. The consistently emerging SARS-CoV-2 variants harboring critical mutations impact the molecular characteristics of viral proteins and display heterogeneous behaviors in immune evasion, transmissibility, and the clinical manifestation during infection, which differ each strain and endow them with distinguished features during populational spread. Several SARS-CoV-2 variants, identified as Variants of Concern (VOC) by the World Health Organization, challenged global efforts on COVID-19 control due to the rapid worldwide spread and enhanced immune evasion from current antibodies and vaccines. Moreover, the recent Omicron variant even exacerbated the global anxiety in the continuous pandemic. Its significant evasion from current medical treatment and disease control even highlights the necessity of combinatory investigation of the mutational pattern and influence of the mutations on viral dynamics against populational immunity, which would greatly facilitate drug and vaccine development and benefit the global public health policymaking. Hence in this review, we summarized the molecular characteristics, immune evasion, and impacts of the SARS-CoV-2 variants and focused on the parallel comparison of different variants in mutational profile, transmissibility and tropism alteration, treatment effectiveness, and clinical manifestations, in order to provide a comprehensive landscape for SARS-CoV-2 variant research.
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Affiliation(s)
- Cong Sun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Chu Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Guo-Long Bu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Lan-Yi Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China. .,Guangdong-Hong Kong Joint Laboratory for RNA Medicine, 510060, Guangzhou, China.
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20
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Intranasal immunization with a proteosome-adjuvanted SARS-CoV-2 spike protein-based vaccine is immunogenic and efficacious in mice and hamsters. Sci Rep 2022; 12:9772. [PMID: 35697917 PMCID: PMC9191540 DOI: 10.1038/s41598-022-13819-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/27/2022] [Indexed: 01/07/2023] Open
Abstract
With the persistence of the SARS-CoV-2 pandemic and the emergence of novel variants, the development of novel vaccine formulations with enhanced immunogenicity profiles could help reduce disease burden in the future. Intranasally delivered vaccines offer a new modality to prevent SARS-CoV-2 infections through the induction of protective immune responses at the mucosal surface where viral entry occurs. Herein, we evaluated a novel protein subunit vaccine formulation containing a resistin-trimerized prefusion Spike antigen (SmT1v3) and a proteosome-based mucosal adjuvant (BDX301) formulated to enable intranasal immunization. In mice, the formulation induced robust antigen-specific IgG and IgA titers, in the blood and lungs, respectively. In addition, the formulations were highly efficacious in a hamster challenge model, reducing viral load and body weight loss. In both models, the serum antibodies had strong neutralizing activity, preventing the cellular binding of the viral Spike protein based on the ancestral reference strain, the Beta (B.1.351) and Delta (B.1.617.2) variants of concern. As such, this intranasal vaccine formulation warrants further development as a novel SARS-CoV-2 vaccine.
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21
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Westendorf K, Žentelis S, Wang L, Foster D, Vaillancourt P, Wiggin M, Lovett E, van der Lee R, Hendle J, Pustilnik A, Sauder JM, Kraft L, Hwang Y, Siegel RW, Chen J, Heinz BA, Higgs RE, Kallewaard NL, Jepson K, Goya R, Smith MA, Collins DW, Pellacani D, Xiang P, de Puyraimond V, Ricicova M, Devorkin L, Pritchard C, O'Neill A, Dalal K, Panwar P, Dhupar H, Garces FA, Cohen CA, Dye JM, Huie KE, Badger CV, Kobasa D, Audet J, Freitas JJ, Hassanali S, Hughes I, Munoz L, Palma HC, Ramamurthy B, Cross RW, Geisbert TW, Menachery V, Lokugamage K, Borisevich V, Lanz I, Anderson L, Sipahimalani P, Corbett KS, Yang ES, Zhang Y, Shi W, Zhou T, Choe M, Misasi J, Kwong PD, Sullivan NJ, Graham BS, Fernandez TL, Hansen CL, Falconer E, Mascola JR, Jones BE, Barnhart BC. LY-CoV1404 (bebtelovimab) potently neutralizes SARS-CoV-2 variants. Cell Rep 2022; 39:110812. [PMID: 35568025 PMCID: PMC9035363 DOI: 10.1016/j.celrep.2022.110812] [Citation(s) in RCA: 228] [Impact Index Per Article: 114.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/24/2022] [Accepted: 04/20/2022] [Indexed: 01/18/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-neutralizing monoclonal antibodies (mAbs) can reduce the risk of hospitalization from coronavirus disease 2019 (COVID-19) when administered early. However, SARS-CoV-2 variants of concern (VOCs) have negatively affected therapeutic use of some authorized mAbs. Using a high-throughput B cell screening pipeline, we isolated LY-CoV1404 (bebtelovimab), a highly potent SARS-CoV-2 spike glycoprotein receptor binding domain (RBD)-specific antibody. LY-CoV1404 potently neutralizes authentic SARS-CoV-2, B.1.1.7, B.1.351, and B.1.617.2. In pseudovirus neutralization studies, LY-CoV1404 potently neutralizes variants, including B.1.1.7, B.1.351, B.1.617.2, B.1.427/B.1.429, P.1, B.1.526, B.1.1.529, and the BA.2 subvariant. Structural analysis reveals that the contact residues of the LY-CoV1404 epitope are highly conserved, except for N439 and N501. The binding and neutralizing activity of LY-CoV1404 is unaffected by the most common mutations at these positions (N439K and N501Y). The broad and potent neutralization activity and the relatively conserved epitope suggest that LY-CoV1404 has the potential to be an effective therapeutic agent to treat all known variants.
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Affiliation(s)
| | | | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Denisa Foster
- Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA
| | - Peter Vaillancourt
- Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA
| | | | - Erica Lovett
- AbCellera Biologics Inc., Vancouver, BC V5Y 0A1, Canada
| | | | - Jörg Hendle
- Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA
| | - Anna Pustilnik
- Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA
| | - J Michael Sauder
- Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA
| | - Lucas Kraft
- AbCellera Biologics Inc., Vancouver, BC V5Y 0A1, Canada
| | - Yuri Hwang
- AbCellera Biologics Inc., Vancouver, BC V5Y 0A1, Canada
| | | | - Jinbiao Chen
- Eli Lilly and Company, Indianapolis, IN 46285, USA
| | | | | | | | - Kevin Jepson
- AbCellera Biologics Inc., Vancouver, BC V5Y 0A1, Canada
| | - Rodrigo Goya
- AbCellera Biologics Inc., Vancouver, BC V5Y 0A1, Canada
| | - Maia A Smith
- AbCellera Biologics Inc., Vancouver, BC V5Y 0A1, Canada
| | | | | | - Ping Xiang
- AbCellera Biologics Inc., Vancouver, BC V5Y 0A1, Canada
| | | | | | | | | | - Aoise O'Neill
- AbCellera Biologics Inc., Vancouver, BC V5Y 0A1, Canada
| | - Kush Dalal
- AbCellera Biologics Inc., Vancouver, BC V5Y 0A1, Canada
| | - Pankaj Panwar
- AbCellera Biologics Inc., Vancouver, BC V5Y 0A1, Canada
| | | | | | - Courtney A Cohen
- U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, MD 21702, USA
| | - John M Dye
- U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, MD 21702, USA
| | - Kathleen E Huie
- U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, MD 21702, USA
| | - Catherine V Badger
- U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, MD 21702, USA
| | - Darwyn Kobasa
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3L5, Canada; University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Jonathan Audet
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3L5, Canada; University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Joshua J Freitas
- Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA
| | - Saleema Hassanali
- Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA
| | - Ina Hughes
- Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA
| | - Luis Munoz
- Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA
| | - Holly C Palma
- Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA
| | | | - Robert W Cross
- University of Manitoba, Winnipeg, MB R3T 2N2, Canada; Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Thomas W Geisbert
- University of Manitoba, Winnipeg, MB R3T 2N2, Canada; Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Vineet Menachery
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Kumari Lokugamage
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Viktoriya Borisevich
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Iliana Lanz
- AbCellera Biologics Inc., Vancouver, BC V5Y 0A1, Canada
| | - Lisa Anderson
- AbCellera Biologics Inc., Vancouver, BC V5Y 0A1, Canada
| | | | - Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Misook Choe
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John Misasi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nancy J Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Carl L Hansen
- AbCellera Biologics Inc., Vancouver, BC V5Y 0A1, Canada
| | | | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bryan E Jones
- Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA.
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22
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McLean G, Kamil J, Lee B, Moore P, Schulz TF, Muik A, Sahin U, Türeci Ö, Pather S. The Impact of Evolving SARS-CoV-2 Mutations and Variants on COVID-19 Vaccines. mBio 2022; 13:e0297921. [PMID: 35352979 PMCID: PMC9040821 DOI: 10.1128/mbio.02979-21] [Citation(s) in RCA: 109] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2022] [Indexed: 12/26/2022] Open
Abstract
The emergence of several new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in recent months has raised concerns around the potential impact on ongoing vaccination programs. Data from clinical trials and real-world evidence suggest that current vaccines remain highly effective against the alpha variant (B.1.1.7), while some vaccines have reduced efficacy and effectiveness against symptomatic disease caused by the beta variant (B.1.351) and the delta variant (B.1.617.2); however, effectiveness against severe disease and hospitalization caused by delta remains high. Although data on the effectiveness of the primary regimen against omicron (B.1.1.529) are limited, booster programs using mRNA vaccines have been shown to restore protection against infection and symptomatic disease (regardless of the vaccine used for the primary regimen) and maintain high effectiveness against hospitalization. However, effectiveness against infection and symptomatic disease wanes with time after the booster dose. Studies have demonstrated reductions of varying magnitude in neutralizing activity of vaccine-elicited antibodies against a range of SARS-CoV-2 variants, with the omicron variant in particular exhibiting partial immune escape. However, evidence suggests that T-cell responses are preserved across vaccine platforms, regardless of variant of concern. Nevertheless, various mitigation strategies are under investigation to address the potential for reduced efficacy or effectiveness against current and future SARS-CoV-2 variants, including modification of vaccines for certain variants (including omicron), multivalent vaccine formulations, and different delivery mechanisms.
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Affiliation(s)
- Gary McLean
- School of Human Sciences, London Metropolitan University and National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Jeremy Kamil
- Louisiana State University Health, Shreveport, Louisiana, USA
| | - Benhur Lee
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Penny Moore
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, The University of the Witwatersrand, Johannesburg, South Africa
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence 2155 RESIST, Hannover, Germany
- German Centre for Infection Research, Hannover-Braunschweig Site, Germany
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23
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The E484K Substitution in a SARS-CoV-2 Spike Protein Subunit Vaccine Resulted in Limited Cross-Reactive Neutralizing Antibody Responses in Mice. Viruses 2022; 14:v14050854. [PMID: 35632595 PMCID: PMC9146450 DOI: 10.3390/v14050854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/14/2022] [Accepted: 04/18/2022] [Indexed: 01/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), especially emerging variants, poses an increased threat to global public health. The significant reduction in neutralization activity against the variants such as B.1.351 in the serum of convalescent patients and vaccinated people calls for the design of new potent vaccines targeting the emerging variant. However, since most vaccines approved and in clinical trials are based on the sequence of the original SARS-CoV-2 strain, the immunogenicity and protective efficacy of vaccines based on the B.1.351 variant remain largely unknown. In this study, we evaluated the immunogenicity, induced neutralization activity, and protective efficacy of wild-type spike protein nanoparticle (S-2P) and mutant spike protein nanoparticle (S-4M-2P) carrying characteristic mutations of B.1.351 variant in mice. Although there was no significant difference in the induction of spike-specific IgG responses in S-2P- and S-4M-2P-immunized mice, neutralizing antibodies elicited by S-4M-2P exhibited noteworthy, narrower breadth of reactivity with SARS-CoV-2 variants compared with neutralizing antibodies elicited by S-2P. Furthermore, the decrease of induced neutralizing antibody breadth at least partly resulted from the amino acid substitution at position 484. Moreover, S-4M-2P vaccination conferred insufficient protection against live SARS-CoV-2 virus infection, while S-2P vaccination gave definite protection against SARS-CoV-2 challenge in mice. Together, our study provides direct evidence that the E484K substitution in a SARS-CoV-2 subunit protein vaccine limited the cross-reactive neutralizing antibody breadth in mice and, more importantly, draws attention to the unfavorable impact of this mutation in spike protein of SARS-CoV-2 variants on the induction of potent neutralizing antibody responses.
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24
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Duarte CM, Ketcheson DI, Eguíluz VM, Agustí S, Fernández-Gracia J, Jamil T, Laiolo E, Gojobori T, Alam I. Rapid evolution of SARS-CoV-2 challenges human defenses. Sci Rep 2022; 12:6457. [PMID: 35440671 PMCID: PMC9017738 DOI: 10.1038/s41598-022-10097-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 03/23/2022] [Indexed: 12/25/2022] Open
Abstract
The race between pathogens and their hosts is a major evolutionary driver, where both reshuffle their genomes to overcome and reorganize the defenses for infection, respectively. Evolutionary theory helps formulate predictions on the future evolutionary dynamics of SARS-CoV-2, which can be monitored through unprecedented real-time tracking of SARS-CoV-2 population genomics at the global scale. Here we quantify the accelerating evolution of SARS-CoV-2 by tracking the SARS-CoV-2 mutation globally, with a focus on the Receptor Binding Domain (RBD) of the spike protein determining infection success. We estimate that the > 820 million people that had been infected by October 5, 2021, produced up to 1021 copies of the virus, with 12 new effective RBD variants appearing, on average, daily. Doubling of the number of RBD variants every 89 days, followed by selection of the most infective variants challenges our defenses and calls for a shift to anticipatory, rather than reactive tactics involving collaborative global sequencing and vaccination.
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Affiliation(s)
- Carlos M Duarte
- Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia. .,Computational Bioscience Research Centre (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
| | - David I Ketcheson
- Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Víctor M Eguíluz
- Instituto de Física Interdisciplinar y Sistemas Complejos IFISC (UIB-CSIC), Palma de Mallorca, Spain
| | - Susana Agustí
- Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Juan Fernández-Gracia
- Instituto de Física Interdisciplinar y Sistemas Complejos IFISC (UIB-CSIC), Palma de Mallorca, Spain
| | - Tahira Jamil
- Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.,Computational Bioscience Research Centre (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Elisa Laiolo
- Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.,Computational Bioscience Research Centre (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Centre (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Intikhab Alam
- Computational Bioscience Research Centre (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
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25
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Argueta LB, Lacko LA, Bram Y, Tada T, Carrau L, Rendeiro AF, Zhang T, Uhl S, Lubor BC, Chandar V, Gil C, Zhang W, Dodson BJ, Bastiaans J, Prabhu M, Houghton S, Redmond D, Salvatore CM, Yang YJ, Elemento O, Baergen RN, tenOever BR, Landau NR, Chen S, Schwartz RE, Stuhlmann H. Inflammatory responses in the placenta upon SARS-CoV-2 infection late in pregnancy. iScience 2022; 25:104223. [PMID: 35434541 PMCID: PMC8996470 DOI: 10.1016/j.isci.2022.104223] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/25/2022] [Accepted: 04/05/2022] [Indexed: 02/06/2023] Open
Abstract
The effect of SARS-CoV-2 infection on placental function is not well understood. Analysis of placentas from women who tested positive at delivery showed SARS-CoV-2 genomic and subgenomic RNA in 22 out of 52 placentas. Placentas from two mothers with symptomatic COVID-19 whose pregnancies resulted in adverse outcomes for the fetuses contained high levels of viral Alpha variant RNA. The RNA was localized to the trophoblasts that cover the fetal chorionic villi in direct contact with maternal blood. The intervillous spaces and villi were infiltrated with maternal macrophages and T cells. Transcriptome analysis showed an increased expression of chemokines and pathways associated with viral infection and inflammation. Infection of placental cultures with live SARS-CoV-2 and spike protein-pseudotyped lentivirus showed infection of syncytiotrophoblast and, in rare cases, endothelial cells mediated by ACE2 and Neuropilin-1. Viruses with Alpha, Beta, and Delta variant spikes infected the placental cultures at significantly greater levels.
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Affiliation(s)
- Lissenya B. Argueta
- Department of Cell and Developmental Biology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Lauretta A. Lacko
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Takuya Tada
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Lucia Carrau
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - André Figueiredo Rendeiro
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Tuo Zhang
- Genomics Resources Facility, Weill Cornell Medicine, New York, NY 10065, USA
| | - Skyler Uhl
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brienne C. Lubor
- Department of Cell and Developmental Biology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Vasuretha Chandar
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Cristianel Gil
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Wei Zhang
- Genomics Resources Facility, Weill Cornell Medicine, New York, NY 10065, USA
| | - Brittany J. Dodson
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jeroen Bastiaans
- Department of Cell and Developmental Biology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Malavika Prabhu
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sean Houghton
- Division of Regenerative Medicine, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - David Redmond
- Division of Regenerative Medicine, Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Christine M. Salvatore
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Weill Cornell Medicine, New York, NY 10065, USA
| | - Yawei J. Yang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Rebecca N. Baergen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Benjamin R. tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nathaniel R. Landau
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA,Corresponding author
| | - Robert E. Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA,Corresponding author
| | - Heidi Stuhlmann
- Department of Cell and Developmental Biology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA,Department of Pediatrics, Weill Cornell Medicine, New York, NY 10065, USA,Corresponding author
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26
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Tada T, Zhou H, Dcosta BM, Samanovic MI, Chivukula V, Herati RS, Hubbard SR, Mulligan MJ, Landau NR. Increased resistance of SARS-CoV-2 Omicron variant to neutralization by vaccine-elicited and therapeutic antibodies. EBioMedicine 2022; 78:103944. [PMID: 35465948 PMCID: PMC9021600 DOI: 10.1016/j.ebiom.2022.103944] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/22/2022] [Accepted: 03/03/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND SARS-CoV-2 vaccines currently authorized for emergency use have been highly successful in preventing infection and lessening disease severity. The vaccines maintain effectiveness against earlier SARS-CoV-2 Variants of Concern but the heavily mutated, highly transmissible Omicron variant presents an obstacle both to vaccine protection and monoclonal antibody therapies. METHODS Pseudotyped lentiviruses were incubated with serum from vaccinated and boosted donors or therapeutic monoclonal antibody and then applied to target cells. After 2 days, luciferase activity was measured in a microplate luminometer. Resistance mutations of the Omicron spike were identified using point-mutated spike protein pseudotypes and mapped onto the three-dimensional spike protein structure. FINDINGS Virus with the Omicron spike protein was 26-fold resistant to neutralization by recovered donor sera and 26-34-fold resistance to Pfizer BNT162b2 and Moderna vaccine-elicited antibodies following two immunizations. A booster immunization increased neutralizing titres against Omicron. Neutralizing titres against Omicron were increased in the sera with a history of prior SARS-CoV-2 infection. Analysis of the therapeutic monoclonal antibodies showed that the Regeneron and Eli Lilly monoclonal antibodies were ineffective against the Omicron pseudotype while Sotrovimab and Evusheld were partially effective. INTERPRETATION The results highlight the benefit of a booster immunization to protect against the Omicron variant and demonstrate the challenge to monoclonal antibody therapy. The decrease in neutralizing titres against Omicron suggest that much of the vaccine efficacy may rely on T cells. FUNDING The work was funded by grants from the NIH to N.R.L. (DA046100, AI122390 and AI120898) and 55 to M.J.M. (UM1AI148574).
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Affiliation(s)
- Takuya Tada
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, Rm 509, New York, NY 10016, USA
| | - Hao Zhou
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, Rm 509, New York, NY 10016, USA
| | - Belinda M Dcosta
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, Rm 509, New York, NY 10016, USA
| | - Marie I Samanovic
- NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Vidya Chivukula
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, Rm 509, New York, NY 10016, USA
| | - Ramin S Herati
- NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Stevan R Hubbard
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Mark J Mulligan
- NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Nathaniel R Landau
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, Rm 509, New York, NY 10016, USA.
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27
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Tada T, Zhou H, Samanovic MI, Dcosta BM, Cornelius A, Herati RS, Mulligan MJ, Landau NR. Neutralization of SARS-CoV-2 Variants by mRNA and Adenoviral Vector Vaccine-Elicited Antibodies. Front Immunol 2022; 13:797589. [PMID: 35350781 PMCID: PMC8957851 DOI: 10.3389/fimmu.2022.797589] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/09/2022] [Indexed: 01/19/2023] Open
Abstract
The increasing prevalence of SARS-CoV-2 variants has raised concerns regarding possible decreases in vaccine effectiveness. Here, neutralizing antibody titers elicited by mRNA-based and adenoviral vector-based vaccines against variant pseudotyped viruses were measured. BNT162b2 and mRNA-1273-elicited antibodies showed modest neutralization resistance against Beta, Delta, Delta plus and Lambda variants whereas Ad26.COV2.S-elicited antibodies from a significant fraction of vaccinated individuals had less neutralizing titer (IC50 <50). The data underscore the importance of surveillance for breakthrough infections that result in severe COVID-19 and suggest a potential benefit by second immunization following Ad26.COV2.S to increase protection from current and future variants.
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Affiliation(s)
- Takuya Tada
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, United States
| | - Hao Zhou
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, United States
| | - Marie I Samanovic
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, United States.,NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, NY, United States
| | - Belinda M Dcosta
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, United States
| | - Amber Cornelius
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, United States.,NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, NY, United States
| | - Ramin S Herati
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, United States.,NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, NY, United States
| | - Mark J Mulligan
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, United States.,Department of Medicine, NYU Grossman School of Medicine, New York, NY, United States.,NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, NY, United States
| | - Nathaniel R Landau
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, United States
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28
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van der Straten K, van Gils MJ, de Taeye SW, de Bree GJ. Optimization of Anti-SARS-CoV-2 Neutralizing Antibody Therapies: Roadmap to Improve Clinical Effectiveness and Implementation. FRONTIERS IN MEDICAL TECHNOLOGY 2022; 4:867982. [PMID: 35419561 PMCID: PMC8996231 DOI: 10.3389/fmedt.2022.867982] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/07/2022] [Indexed: 12/11/2022] Open
Abstract
One of the major breakthroughs to combat the current Coronavirus Disease 2019 (COVID-19) pandemic has been the development of highly effective vaccines against the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Still, alternatives are needed for individuals who are at high risk of developing severe COVID-19 and are not protected by vaccination. Monoclonal antibodies against the spike protein of SARS-CoV-2 have been shown to be effective as prophylaxis and treatment against COVID-19. However, the emergence of variants of concern (VOCs) challenges the efficacy of antibody therapies. This review describes the neutralization resistance of the clinically-approved monoclonal antibody therapies against the Alpha (B.1.1.7), Beta (B.1.351), Gamma (P1), Delta (B.1.617.2), and the Omicron (B.1.1.529) variants. To guide the development of monoclonal antibody therapies and to anticipate on the continuous evolution of SARS-CoV-2, we highlight different strategies to broaden the antibody activity by targeting more conserved epitopes and/or simultaneously targeting multiple sites of vulnerability of the virus. This review further describes the contribution of antibody Fc effector functions to optimize the antibody efficacy. In addition, the main route of SARS-CoV-2 antibody administration is currently intravenously and dictates a monthly injection when used as prophylactic. Therefore, we discusses the concept of long-acting antibodies (LAABs) and non-intravenously routes of antibody administration in order to broaden the clinical applicability of antibody therapies.
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Affiliation(s)
- Karlijn van der Straten
- Department of Medical Microbiology and Infection Prevention, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Internal Medicine, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Marit J. van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Steven W. de Taeye
- Department of Medical Microbiology and Infection Prevention, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Godelieve J. de Bree
- Department of Internal Medicine, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- *Correspondence: Godelieve J. de Bree
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29
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Fung KM, Lai SJ, Lin TL, Tseng TS. Antigen–Antibody Complex-Guided Exploration of the Hotspots Conferring the Immune-Escaping Ability of the SARS-CoV-2 RBD. Front Mol Biosci 2022; 9:797132. [PMID: 35392535 PMCID: PMC8981523 DOI: 10.3389/fmolb.2022.797132] [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] [Received: 10/18/2021] [Accepted: 03/02/2022] [Indexed: 11/24/2022] Open
Abstract
The COVID-19 pandemic resulting from the spread of SARS-CoV-2 spurred devastating health and economic crises around the world. Neutralizing antibodies and licensed vaccines were developed to combat COVID-19, but progress was slow. In addition, variants of the receptor-binding domain (RBD) of the spike protein confer resistance of SARS-CoV-2 to neutralizing antibodies, nullifying the possibility of human immunity. Therefore, investigations into the RBD mutations that disrupt neutralization through convalescent antibodies are urgently required. In this study, we comprehensively and systematically investigated the binding stability of RBD variants targeting convalescent antibodies and revealed that the RBD residues F456, F490, L452, L455, and K417 are immune-escaping hotspots, and E484, F486, and N501 are destabilizing residues. Our study also explored the possible modes of actions of emerging SARS-CoV-2 variants. All results are consistent with experimental observations of attenuated antibody neutralization and clinically emerging SARS-CoV-2 variants. We identified possible immune-escaping hotspots that could further promote resistance to convalescent antibodies. The results provide valuable information for developing and designing novel monoclonal antibody drugs to combat emerging SARS-CoV-2 variants.
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Affiliation(s)
- Kit-Man Fung
- Academia Sinica, Institute of Biological Chemistry, Taipei, Taiwan
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Shu-Jung Lai
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Tzu-Lu Lin
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Tien-Sheng Tseng
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
- *Correspondence: Tien-Sheng Tseng,
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30
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Noori M, Nejadghaderi SA, Arshi S, Carson‐Chahhoud K, Ansarin K, Kolahi A, Safiri S. Potency of BNT162b2 and mRNA-1273 vaccine-induced neutralizing antibodies against severe acute respiratory syndrome-CoV-2 variants of concern: A systematic review of in vitro studies. Rev Med Virol 2022; 32:e2277. [PMID: 34286893 PMCID: PMC8420542 DOI: 10.1002/rmv.2277] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 12/23/2022]
Abstract
BNT162b2 and mRNA-1273 are two types of mRNA-based vaccine platforms that have received emergency use authorization. The emergence of novel severe acute respiratory syndrome (SARS-CoV-2) variants has raised concerns of reduced sensitivity to neutralization by their elicited antibodies. We aimed to systematically review the most recent in vitro studies evaluating the effectiveness of BNT162b2 and mRNA-1273 induced neutralizing antibodies against SARS-CoV-2 variants of concern. We searched PubMed, Scopus, and Web of Science in addition to bioRxiv and medRxiv with terms including 'SARS-CoV-2', 'BNT162b2', 'mRNA-1273', and 'neutralizing antibody' up to June 29, 2021. A modified version of the Consolidated Standards of Reporting Trials (CONSORT) checklist was used for assessing included study quality. A total 36 in vitro studies meeting the eligibility criteria were included in this systematic review. B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), and B.1.617.2 (Delta) are four SARS-CoV-2 variants that have recently been identified as variants of concern. Included studies implemented different methods regarding pseudovirus or live virus neutralization assays for measuring neutralization titres against utilized viruses. After two dose vaccination by BNT162b2 or mRNA-1273, the B.1.351 variant had the least sensitivity to neutralizing antibodies, while B.1.1.7 variant had the most sensitivity; that is, it was better neutralized relative to the comparator strain. P.1 and B.1.617.2 variants had an intermediate level of impaired naturalization activity of antibodies elicited by prior vaccination. Our review suggests that immune sera derived from vaccinated individuals might show reduced protection of individuals immunized with mRNA vaccines against more recent SARS-CoV-2 variants of concern.
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Affiliation(s)
- Maryam Noori
- Student Research CommitteeSchool of MedicineIran University of Medical SciencesTehranIran
| | - Seyed Aria Nejadghaderi
- School of MedicineShahid Beheshti University of Medical SciencesTehranIran
- Systematic Review and Meta‐analysis Expert Group (SRMEG)Universal Scientific Education and Research Network (USERN)TehranIran
| | - Shahnam Arshi
- Social Determinants of Health Research CenterShahid Beheshti University of Medical SciencesTehranIran
| | - Kristin Carson‐Chahhoud
- Australian Centre for Precision HealthAllied Health and Human PerformanceUniversity of South AustraliaSouth AustraliaAustralia
- School of MedicineThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Khalil Ansarin
- Rahat Breath and Sleep Research CenterTabriz University of Medical SciencesTabrizIran
- Tuberculosis and Lung Disease Research CenterTabriz University of Medical SciencesTabrizIran
| | - Ali‐Asghar Kolahi
- Social Determinants of Health Research CenterShahid Beheshti University of Medical SciencesTehranIran
| | - Saeid Safiri
- Tuberculosis and Lung Disease Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Community MedicineFaculty of MedicineTabriz University of Medical SciencesTabrizIran
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31
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McCallum M, Czudnochowski N, Rosen LE, Zepeda SK, Bowen JE, Walls AC, Hauser K, Joshi A, Stewart C, Dillen JR, Powell AE, Croll TI, Nix J, Virgin HW, Corti D, Snell G, Veesler D. Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement. Science 2022; 375:864-868. [PMID: 35076256 PMCID: PMC9427005 DOI: 10.1126/science.abn8652] [Citation(s) in RCA: 336] [Impact Index Per Article: 168.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern evades antibody-mediated immunity that comes from vaccination or infection with earlier variants due to accumulation of numerous spike mutations. To understand the Omicron antigenic shift, we determined cryo-electron microscopy and x-ray crystal structures of the spike protein and the receptor-binding domain bound to the broadly neutralizing sarbecovirus monoclonal antibody (mAb) S309 (the parent mAb of sotrovimab) and to the human ACE2 receptor. We provide a blueprint for understanding the marked reduction of binding of other therapeutic mAbs that leads to dampened neutralizing activity. Remodeling of interactions between the Omicron receptor-binding domain and human ACE2 likely explains the enhanced affinity for the host receptor relative to the ancestral virus.
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MESH Headings
- Amino Acid Substitution
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/metabolism
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/metabolism
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Antigenic Drift and Shift
- Broadly Neutralizing Antibodies/chemistry
- Broadly Neutralizing Antibodies/immunology
- Broadly Neutralizing Antibodies/metabolism
- Cryoelectron Microscopy
- Crystallography, X-Ray
- Humans
- Immune Evasion
- Models, Molecular
- Mutation
- Protein Binding
- Protein Conformation
- Protein Domains/genetics
- Protein Interaction Domains and Motifs/genetics
- Receptors, Coronavirus/chemistry
- Receptors, Coronavirus/metabolism
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/physiology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
- Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | | | - Samantha K. Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | | | - Anshu Joshi
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | | | - Tristan I. Croll
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge, UK
| | - Jay Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Herbert W. Virgin
- Vir Biotechnology, San Francisco, CA 94158, USA
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis MO 63110
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas TX 75390
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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32
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Counoupas C, Pino P, Stella AO, Ashley C, Lukeman H, Bhattacharyya ND, Tada T, Anchisi S, Metayer C, Martinis J, Aggarwal A, Dcosta BM, Britton WJ, Kint J, Wurm MJ, Landau NR, Steain M, Turville SG, Wurm FM, David SA, Triccas JA. High-Titer Neutralizing Antibodies against the SARS-CoV-2 Delta Variant Induced by Alhydroxyquim-II-Adjuvanted Trimeric Spike Antigens. Microbiol Spectr 2022; 10:e0169521. [PMID: 35171046 PMCID: PMC8849074 DOI: 10.1128/spectrum.01695-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/13/2022] [Indexed: 12/23/2022] Open
Abstract
Global control of COVID-19 will require the deployment of vaccines capable of inducing long-term protective immunity against SARS-CoV-2 variants. In this report, we describe an adjuvanted subunit candidate vaccine that affords elevated, sustained, and cross-variant SARS-CoV-2 neutralizing antibodies (NAbs) in multiple animal models. Alhydroxiquim-II is a Toll-Like Receptor (TLR) 7/8 small-molecule agonist chemisorbed on aluminum hydroxide (Alhydrogel). Vaccination with Alhydroxiquim-II combined with a stabilized, trimeric form of the SARS-CoV-2 spike protein (termed CoVac-II) resulted in high-titer NAbs in mice, with no decay in responses over an 8-month period. NAbs from sera of CoVac-II-immunized mice, horses and rabbits were broadly neutralizing against SARS-CoV-2 variants. Boosting long-term CoVac-II-immunized mice with adjuvanted spike protein from the Beta variant markedly increased levels of NAb titers against multiple SARS-CoV-2 variants; notably, high titers against the Delta variant were observed. These data strongly support the clinical assessment of Alhydroxiquim-II-adjuvanted spike proteins to protect against SARS-CoV-2 variants of concern. IMPORTANCE There is an urgent need for next-generation COVID-19 vaccines that are safe, demonstrate high protective efficacy against SARS-CoV-2 variants and can be manufactured at scale. We describe a vaccine candidate (CoVac-II) that is based on stabilized, trimeric spike antigen produced in an optimized, scalable and chemically defined production process. CoVac-II demonstrates strong and persistent immunity after vaccination of mice, and is highly immunogenic in multiple animal models, including rabbits and horses. We further show that prior immunity can be boosted using a recombinant spike antigen from the Beta variant; importantly, plasma from boosted mice effectively neutralize multiple SARS-CoV-2 variants in vitro, including Delta. The strong humoral and Th1-biased immunogenicity of CoVac-II is driven by use of Alhydroxiquim-II (AHQ-II), the first adjuvant in an authorized vaccine that acts through the dual Toll-like receptor (TLR)7 and TLR8 pathways, as part of the Covaxin vaccine. Our data suggest AHQ-II/spike protein combinations could constitute safe, affordable, and mass-manufacturable COVID-19 vaccines for global distribution.
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Affiliation(s)
- Claudio Counoupas
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, New South Wales, Australia
- Tuberculosis Research Program, Centenary Institute, Sydney, New South Wales, Australia
| | | | - Alberto O. Stella
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Caroline Ashley
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, New South Wales, Australia
| | - Hannah Lukeman
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, New South Wales, Australia
| | - Nayan D. Bhattacharyya
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, New South Wales, Australia
| | - Takuya Tada
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
| | | | | | | | - Anupriya Aggarwal
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Belinda M. Dcosta
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Warwick J. Britton
- Tuberculosis Research Program, Centenary Institute, Sydney, New South Wales, Australia
| | | | | | - Nathaniel R. Landau
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Megan Steain
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, New South Wales, Australia
| | - Stuart G. Turville
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Florian M. Wurm
- ExcellGene SA, Monthey, Switzerland
- Life Science Faculty, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | | | - James A. Triccas
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, New South Wales, Australia
- Sydney Institute for Infectious Diseases and the Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales, Australia
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33
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Uwamino Y, Yokoyama T, Shimura T, Nishimura T, Sato Y, Wakui M, Kosaki K, Hasegawa N, Murata M. The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals. Vaccine 2022; 40:1928-1931. [PMID: 35183387 PMCID: PMC8841208 DOI: 10.1016/j.vaccine.2022.02.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/14/2021] [Accepted: 02/09/2022] [Indexed: 10/26/2022]
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34
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Zhou W, Xu C, Wang P, Anashkina AA, Jiang Q. Impact of mutations in SARS-COV-2 spike on viral infectivity and antigenicity. Brief Bioinform 2022; 23:bbab375. [PMID: 34518867 PMCID: PMC8499914 DOI: 10.1093/bib/bbab375] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/09/2021] [Accepted: 08/23/2021] [Indexed: 12/23/2022] Open
Abstract
Since the outbreak of SARS-CoV-2, the etiologic agent of the COVID-19 pandemic, the viral genome has acquired numerous mutations with the potential to alter the viral infectivity and antigenicity. Part of mutations in SARS-CoV-2 spike protein has conferred virus the ability to spread more quickly and escape from the immune response caused by the monoclonal neutralizing antibody or vaccination. Herein, we summarize the spatiotemporal distribution of mutations in spike protein, and present recent efforts and progress in investigating the impacts of those mutations on viral infectivity and antigenicity. As mutations continue to emerge in SARS-CoV-2, we strive to provide systematic evaluation of mutations in spike protein, which is vitally important for the subsequent improvement of vaccine and therapeutic neutralizing antibody strategies.
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Affiliation(s)
- Wenyang Zhou
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Chang Xu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Pingping Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | | | - Qinghua Jiang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
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35
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Tada T, Zhou H, Dcosta BM, Samanovic MI, Cornelius A, Herati RS, Mulligan MJ, Landau NR. High-titer neutralization of Mu and C.1.2 SARS-CoV-2 variants by vaccine-elicited antibodies of previously infected individuals. Cell Rep 2022; 38:110237. [PMID: 34982967 PMCID: PMC8687746 DOI: 10.1016/j.celrep.2021.110237] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/16/2021] [Accepted: 12/16/2021] [Indexed: 12/21/2022] Open
Abstract
Recently identified severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants Mu and C.1.2 have spike proteins with mutations that may confer resistance to natural and vaccine-elicited antibodies. Analysis of neutralizing antibody titers in the sera of vaccinated individuals without previous history of infection and from convalescent individuals show partial resistance of the viruses. In contrast, sera from individuals with a previous history of SARS-CoV-2 infection who were subsequently vaccinated neutralize variants with titers 4- to 11-fold higher, providing a rationale for vaccination of individuals with previous infection. The heavily mutated C.1.2 spike is the most antibody neutralization-resistant spike to date; however, the avidity of C.1.2 spike protein for angiotensin-converting enzyme 2 (ACE2) is low. This finding suggests that the virus evolved to escape the humoral response but has a decrease in fitness, suggesting that it may cause milder disease or be less transmissible. It may be difficult for the spike protein to evolve to escape neutralizing antibodies while maintaining high affinity for ACE2.
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Affiliation(s)
- Takuya Tada
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Hao Zhou
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Belinda M Dcosta
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Marie I Samanovic
- NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Amber Cornelius
- NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Ramin S Herati
- NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Mark J Mulligan
- NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Nathaniel R Landau
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA.
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36
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Hanke L, Das H, Sheward DJ, Perez Vidakovics L, Urgard E, Moliner-Morro A, Kim C, Karl V, Pankow A, Smith NL, Porebski B, Fernandez-Capetillo O, Sezgin E, Pedersen GK, Coquet JM, Hällberg BM, Murrell B, McInerney GM. A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo. Nat Commun 2022; 13:155. [PMID: 35013189 PMCID: PMC8748511 DOI: 10.1038/s41467-021-27610-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 11/30/2021] [Indexed: 01/04/2023] Open
Abstract
Antibodies binding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike have therapeutic promise, but emerging variants show the potential for virus escape. This emphasizes the need for therapeutic molecules with distinct and novel neutralization mechanisms. Here we describe the isolation of a nanobody that interacts simultaneously with two RBDs from different spike trimers of SARS-CoV-2, rapidly inducing the formation of spike trimer-dimers leading to the loss of their ability to attach to the host cell receptor, ACE2. We show that this nanobody potently neutralizes SARS-CoV-2, including the beta and delta variants, and cross-neutralizes SARS-CoV. Furthermore, we demonstrate the therapeutic potential of the nanobody against SARS-CoV-2 and the beta variant in a human ACE2 transgenic mouse model. This naturally elicited bispecific monomeric nanobody establishes an uncommon strategy for potent inactivation of viral antigens and represents a promising antiviral against emerging SARS-CoV-2 variants.
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Affiliation(s)
- Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Laura Perez Vidakovics
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Egon Urgard
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ainhoa Moliner-Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Vivien Karl
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alec Pankow
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Natalie L Smith
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Bartlomiej Porebski
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Oscar Fernandez-Capetillo
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Gabriel K Pedersen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jonathan M Coquet
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Karolinska Institutet VR-RÅC, Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany.
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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Hanke L, Das H, Sheward DJ, Perez Vidakovics L, Urgard E, Moliner-Morro A, Kim C, Karl V, Pankow A, Smith NL, Porebski B, Fernandez-Capetillo O, Sezgin E, Pedersen GK, Coquet JM, Hällberg BM, Murrell B, McInerney GM. A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo. Nat Commun 2022. [PMID: 35013189 DOI: 10.1101/2021.03.20.436243v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023] Open
Abstract
Antibodies binding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike have therapeutic promise, but emerging variants show the potential for virus escape. This emphasizes the need for therapeutic molecules with distinct and novel neutralization mechanisms. Here we describe the isolation of a nanobody that interacts simultaneously with two RBDs from different spike trimers of SARS-CoV-2, rapidly inducing the formation of spike trimer-dimers leading to the loss of their ability to attach to the host cell receptor, ACE2. We show that this nanobody potently neutralizes SARS-CoV-2, including the beta and delta variants, and cross-neutralizes SARS-CoV. Furthermore, we demonstrate the therapeutic potential of the nanobody against SARS-CoV-2 and the beta variant in a human ACE2 transgenic mouse model. This naturally elicited bispecific monomeric nanobody establishes an uncommon strategy for potent inactivation of viral antigens and represents a promising antiviral against emerging SARS-CoV-2 variants.
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Affiliation(s)
- Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Laura Perez Vidakovics
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Egon Urgard
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ainhoa Moliner-Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Vivien Karl
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alec Pankow
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Natalie L Smith
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Bartlomiej Porebski
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Oscar Fernandez-Capetillo
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Gabriel K Pedersen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jonathan M Coquet
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Karolinska Institutet VR-RÅC, Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany.
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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38
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Mukhopadhyay L, Gupta N, Yadav PD, Aggarwal N. Neutralization assays for SARS-CoV-2: Implications for assessment of protective efficacy of COVID-19 vaccines. Indian J Med Res 2022; 155:105-122. [PMID: 35859437 PMCID: PMC9552365 DOI: 10.4103/ijmr.ijmr_2544_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The WHO emergency use-listed (EUL) COVID-19 vaccines were developed against early strains of SARS-CoV-2. With the emergence of SARS-CoV-2 variants of concern (VOCs) - Alpha, Beta, Gamma, Delta and Omicron, it is necessary to assess the neutralizing activity of these vaccines against the VOCs. PubMed and preprint platforms were searched for literature on neutralizing activity of serum from WHO EUL vaccine recipients, against the VOCs, using appropriate search terms till November 30, 2021. Our search yielded 91 studies meeting the inclusion criteria. The analysis revealed a drop of 0-8.9-fold against Alpha variant, 0.3-42.4-fold against Beta variant, 0-13.8-fold against Gamma variant and 1.35-20-fold against Delta variant in neutralization titres of serum from the WHO EUL COVID-19 vaccine recipients, as compared to early SARS-CoV-2 isolates. The wide range of variability was due to differences in the choice of virus strains selected for neutralization assays (pseudovirus or live virus), timing of serum sample collection after the final dose of vaccine (day 0 to 8 months) and sample size (ranging from 5 to 470 vaccinees). The reasons for this variation have been discussed and the possible way forward to have uniformity across neutralization assays in different laboratories have been described, which will generate reliable data. Though in vitro neutralization studies are a valuable tool to estimate the performance of vaccines against the backdrop of emerging variants, the results must be interpreted with caution and corroborated with field-effectiveness studies.
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Affiliation(s)
- Labanya Mukhopadhyay
- Virology Unit, Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Nivedita Gupta
- Virology Unit, Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Pragya D Yadav
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Neeraj Aggarwal
- Virology Unit, Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
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39
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Showers WM, Leach SM, Kechris K, Strong M. Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 97:105153. [PMID: 34801754 PMCID: PMC8600767 DOI: 10.1016/j.meegid.2021.105153] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 11/05/2021] [Accepted: 11/16/2021] [Indexed: 01/18/2023]
Abstract
Amid the ongoing COVID-19 pandemic, it has become increasingly important to monitor the mutations that arise in the SARS-CoV-2 virus, to prepare public health strategies and guide the further development of vaccines and therapeutics. The spike (S) protein and the proteins comprising the RNA-Dependent RNA Polymerase (RdRP) are key vaccine and drug targets, respectively, making mutation surveillance of these proteins of great importance. Full protein sequences were downloaded from the GISAID database, aligned, and the variants identified. 437,006 unique viral genomes were analyzed. Polymorphisms in the protein sequence were investigated and examined longitudinally to identify sequence and strain variants appearing between January 5th, 2020 and January 16th, 2021. A structural analysis was also performed to investigate mutations in the receptor binding domain and the N-terminal domain of the spike protein. Within the spike protein, there were 766 unique mutations observed in the N-terminal domain and 360 in the receptor binding domain. Four residues that directly contact ACE2 were mutated in more than 100 sequences, including positions K417, Y453, S494, and N501. Within the furin cleavage site of the spike protein, a high degree of conservation was observed, but the P681H mutation was observed in 10.47% of sequences analyzed. Within the RNA dependent RNA polymerase complex proteins, 327 unique mutations were observed in Nsp8, 166 unique mutations were observed in Nsp7, and 1157 unique mutations were observed in Nsp12. Only 4 sequences analyzed contained mutations in the 9 residues that directly interact with the therapeutic Remdesivir, suggesting limited mutations in drug interacting residues. The identification of new variants emphasizes the need for further study on the effects of the mutations and the implications of increased prevalence, particularly for vaccine or therapeutic efficacy.
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Affiliation(s)
- William M Showers
- University of Colorado Anschutz Medical Campus, 13001 East 17th Place, Aurora, CO, USA; Center for Genes, Environment, and Health, National Jewish Health, Smith Building, Room A651, 1400 Jackson Street, Denver, CO, USA.
| | - Sonia M Leach
- University of Colorado Anschutz Medical Campus, 13001 East 17th Place, Aurora, CO, USA; Center for Genes, Environment, and Health, National Jewish Health, Smith Building, Room A651, 1400 Jackson Street, Denver, CO, USA
| | - Katerina Kechris
- University of Colorado Anschutz Medical Campus, 13001 East 17th Place, Aurora, CO, USA
| | - Michael Strong
- University of Colorado Anschutz Medical Campus, 13001 East 17th Place, Aurora, CO, USA; Center for Genes, Environment, and Health, National Jewish Health, Smith Building, Room A651, 1400 Jackson Street, Denver, CO, USA
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40
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Wu K, Choi A, Koch M, Elbashir S, Ma L, Lee D, Woods A, Henry C, Palandjian C, Hill A, Jani H, Quinones J, Nunna N, O'Connell S, McDermott AB, Falcone S, Narayanan E, Colpitts T, Bennett H, Corbett KS, Seder R, Graham BS, Stewart-Jones GBE, Carfi A, Edwards DK. Variant SARS-CoV-2 mRNA vaccines confer broad neutralization as primary or booster series in mice. Vaccine 2021; 39:7394-7400. [PMID: 34815117 PMCID: PMC8572694 DOI: 10.1016/j.vaccine.2021.11.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/04/2021] [Accepted: 11/01/2021] [Indexed: 12/12/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of a global pandemic. Safe and effective COVID-19 vaccines are now available, including mRNA-1273, which has shown 94% efficacy in prevention of symptomatic COVID-19 disease. However, the emergence of SARS-CoV-2 variants has led to concerns of viral escape from vaccine-induced immunity. Several variants have shown decreased susceptibility to neutralization by vaccine-induced immunity, most notably B.1.351 (Beta), although the overall impact on vaccine efficacy remains to be determined. Here, we present the initial evaluation in mice of 2 updated mRNA vaccines designed to target SARS-CoV-2 variants: (1) monovalent mRNA-1273.351 encodes for the spike protein found in B.1.351 and (2) mRNA-1273.211 comprising a 1:1 mix of mRNA-1273 and mRNA-1273.351. Both vaccines were evaluated as a 2-dose primary series in mice; mRNA-1273.351 was also evaluated as a booster dose in animals previously vaccinated with mRNA-1273. The results demonstrated that a primary vaccination series of mRNA-1273.351 was effective at increasing neutralizing antibody titers against B.1.351, while mRNA-1273.211 was effective at providing broad cross-variant neutralization. A third (booster) dose of mRNA-1273.351 significantly increased both wild-type and B.1.351-specific neutralization titers. Both mRNA-1273.351 and mRNA-1273.211 are being evaluated in pre-clinical challenge and clinical studies.
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Affiliation(s)
- Kai Wu
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA.
| | - Angela Choi
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - Matthew Koch
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - Sayda Elbashir
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - LingZhi Ma
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - Diana Lee
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - Angela Woods
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - Carole Henry
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | | | - Anna Hill
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - Hardik Jani
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - Julian Quinones
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - Naveen Nunna
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - Sarah O'Connell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 10 Center Dr, Bethesda, MD 20814, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 10 Center Dr, Bethesda, MD 20814, USA
| | | | | | - Tonya Colpitts
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | | | - Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 10 Center Dr, Bethesda, MD 20814, USA
| | - Robert Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 10 Center Dr, Bethesda, MD 20814, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 10 Center Dr, Bethesda, MD 20814, USA
| | | | - Andrea Carfi
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - Darin K Edwards
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA.
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41
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Lubin JH, Markosian C, Balamurugan D, Pasqualini R, Arap W, Burley SK, Khare SD. Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.12.472313. [PMID: 34931193 PMCID: PMC8687476 DOI: 10.1101/2021.12.12.472313] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
There is enormous ongoing interest in characterizing the binding properties of the SARS-CoV-2 Omicron Variant of Concern (VOC) (B.1.1.529), which continues to spread towards potential dominance worldwide. To aid these studies, based on the wealth of available structural information about several SARS-CoV-2 variants in the Protein Data Bank (PDB) and a modeling pipeline we have previously developed for tracking the ongoing global evolution of SARS-CoV-2 proteins, we provide a set of computed structural models (henceforth models) of the Omicron VOC receptor-binding domain (omRBD) bound to its corresponding receptor Angiotensin-Converting Enzyme (ACE2) and a variety of therapeutic entities, including neutralizing and therapeutic antibodies targeting previously-detected viral strains. We generated bound omRBD models using both experimentally-determined structures in the PDB as well as machine learningbased structure predictions as starting points. Examination of ACE2-bound omRBD models reveals an interdigitated multi-residue interaction network formed by omRBD-specific substituted residues (R493, S496, Y501, R498) and ACE2 residues at the interface, which was not present in the original Wuhan-Hu-1 RBD-ACE2 complex. Emergence of this interaction network suggests optimization of a key region of the binding interface, and positive cooperativity among various sites of residue substitutions in omRBD mediating ACE2 binding. Examination of neutralizing antibody complexes for Barnes Class 1 and Class 2 antibodies modeled with omRBD highlights an overall loss of interfacial interactions (with gain of new interactions in rare cases) mediated by substituted residues. Many of these substitutions have previously been found to independently dampen or even ablate antibody binding, and perhaps mediate antibody-mediated neutralization escape ( e.g ., K417N). We observe little compensation of corresponding interaction loss at interfaces when potential escape substitutions occur in combination. A few selected antibodies ( e.g ., Barnes Class 3 S309), however, feature largely unaltered or modestly affected protein-protein interfaces. While we stress that only qualitative insights can be obtained directly from our models at this time, we anticipate that they can provide starting points for more detailed and quantitative computational characterization, and, if needed, redesign of monoclonal antibodies for targeting the Omicron VOC Spike protein. In the broader context, the computational pipeline we developed provides a framework for rapidly and efficiently generating retrospective and prospective models for other novel variants of SARS-CoV-2 bound to entities of virological and therapeutic interest, in the setting of a global pandemic.
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Affiliation(s)
- Joseph H. Lubin
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
| | - Christopher Markosian
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - D. Balamurugan
- Office of Advanced Research Computing, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
| | - Renata Pasqualini
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Wadih Arap
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Hematology/Oncology, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Stephen K. Burley
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
- RCSB Protein Data Bank, San Diego Supercomputer Center and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92067
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
| | - Sagar D. Khare
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
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42
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Neerukonda SN, Vassell R, Lusvarghi S, Wang R, Echegaray F, Bentley L, Eakin AE, Erlandson KJ, Katzelnick LC, Weiss CD, Wang W. SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Viruses 2021; 13:2485. [PMID: 34960755 PMCID: PMC8707919 DOI: 10.3390/v13122485] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 12/24/2022] Open
Abstract
The SARS-CoV-2 B.1.617 lineage variants, Kappa (B.1.617.1) and Delta (B.1.617.2, AY) emerged during the second wave of infections in India, but the Delta variants have become dominant worldwide and continue to evolve. Here, we compared B.1.617 variants for neutralization resistance by convalescent sera, mRNA vaccine-elicited sera, and therapeutic neutralizing antibodies using a pseudovirus neutralization assay. B.1.617.1, B.1.617.2, and AY.1 pseudoviruses showed a modest 1.5- to 4.4-fold reduction in neutralization by convalescent sera and vaccine-elicited sera. In comparison, similar modest reductions were also observed for C.37, P.1, R.1, and B.1.526 pseudoviruses, but 7- and 16-fold reductions for vaccine-elicited and convalescent sera, respectively, were seen for B.1.351 pseudoviruses. Among twenty-three therapeutic antibodies tested, four antibodies showed either complete or partial loss of neutralization against B.1.617.2 pseudoviruses and six antibodies showed either complete or partial loss of neutralization against B.1.617.1 and AY.1 pseudoviruses. Our results indicate that the current mRNA-based vaccines will likely remain effective in protecting against B.1.617 variants. Finally, the P681R substitution confers efficient cleavage of B.1.617 variants' spike proteins and the spike of Delta variants exhibited greater sensitivity to soluble ACE2 neutralization, as well as fusogenic activity, which may contribute to enhanced spread of Delta variants.
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Affiliation(s)
- Sabari Nath Neerukonda
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA; (S.N.N.); (R.V.); (S.L.); (R.W.)
| | - Russell Vassell
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA; (S.N.N.); (R.V.); (S.L.); (R.W.)
| | - Sabrina Lusvarghi
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA; (S.N.N.); (R.V.); (S.L.); (R.W.)
| | - Richard Wang
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA; (S.N.N.); (R.V.); (S.L.); (R.W.)
| | - Fernando Echegaray
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (F.E.); (L.C.K.)
| | - Lisa Bentley
- Office of the Assistance Secretary for Preparedness and Response, U.S. Department of Health and Human Services, Washington, DC 20201, USA;
| | - Ann E. Eakin
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Rockville, MD 20892, USA;
| | - Karl J. Erlandson
- Influenza and Emerging Infectious Diseases Division, Biomedical Advanced Research and Development Authority, U.S. Department of Health and Human Services, Washington, DC 20201, USA;
| | - Leah C. Katzelnick
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (F.E.); (L.C.K.)
| | - Carol D. Weiss
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA; (S.N.N.); (R.V.); (S.L.); (R.W.)
| | - Wei Wang
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA; (S.N.N.); (R.V.); (S.L.); (R.W.)
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43
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Tao K, Tzou PL, Nouhin J, Gupta RK, de Oliveira T, Kosakovsky Pond SL, Fera D, Shafer RW. The biological and clinical significance of emerging SARS-CoV-2 variants. Nat Rev Genet 2021; 22:757-773. [PMID: 34535792 PMCID: PMC8447121 DOI: 10.1038/s41576-021-00408-x] [Citation(s) in RCA: 613] [Impact Index Per Article: 204.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 12/13/2022]
Abstract
The past several months have witnessed the emergence of SARS-CoV-2 variants with novel spike protein mutations that are influencing the epidemiological and clinical aspects of the COVID-19 pandemic. These variants can increase rates of virus transmission and/or increase the risk of reinfection and reduce the protection afforded by neutralizing monoclonal antibodies and vaccination. These variants can therefore enable SARS-CoV-2 to continue its spread in the face of rising population immunity while maintaining or increasing its replication fitness. The identification of four rapidly expanding virus lineages since December 2020, designated variants of concern, has ushered in a new stage of the pandemic. The four variants of concern, the Alpha variant (originally identified in the UK), the Beta variant (originally identified in South Africa), the Gamma variant (originally identified in Brazil) and the Delta variant (originally identified in India), share several mutations with one another as well as with an increasing number of other recently identified SARS-CoV-2 variants. Collectively, these SARS-CoV-2 variants complicate the COVID-19 research agenda and necessitate additional avenues of laboratory, epidemiological and clinical research.
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Affiliation(s)
- Kaiming Tao
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Philip L Tzou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Janin Nouhin
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Ravindra K Gupta
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa
| | | | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA, USA
| | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
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44
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Immune response against SARS-CoV-2 variants: the role of neutralization assays. NPJ Vaccines 2021; 6:142. [PMID: 34845231 PMCID: PMC8630184 DOI: 10.1038/s41541-021-00404-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 11/03/2021] [Indexed: 12/17/2022] Open
Abstract
Since the emergence of the novel coronavirus SARS-CoV-2 in late 2019, the COVID-19 pandemic has hindered social life and global economic activity. As of July 2021, SARS-CoV-2 has caused over four million deaths. The rapid spread and high mortality of the disease demanded the international scientific community to develop effective vaccines in a matter of months. However, unease about vaccine efficacy has arisen with the spread of the SARS-CoV-2 variants of concern (VOCs). Time- and cost-efficient in vitro neutralization assays are widely used to measure neutralizing antibody responses against VOCs. However, the extent to which in vitro neutralization reflects protection from infection remains unclear. Here, we describe common neutralization assays based on infectious and pseudotyped viruses and evaluate their role in testing neutralizing responses against new SARS-CoV-2 variants. Additionally, we briefly review the recent findings on the immune response elicited by available vaccines against major SARS-CoV-2 variants, including Alpha, Beta, Gamma, and Delta.
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45
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Zhang Y, Banga Ndzouboukou JL, Gan M, Lin X, Fan X. Immune Evasive Effects of SARS-CoV-2 Variants to COVID-19 Emergency Used Vaccines. Front Immunol 2021; 12:771242. [PMID: 34880867 PMCID: PMC8645832 DOI: 10.3389/fimmu.2021.771242] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/29/2021] [Indexed: 12/30/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic is a serious threat to global public health and social and economic development. Various vaccine platforms have been developed rapidly and unprecedentedly, and at least 16 vaccines receive emergency use authorization (EUA). However, the causative pathogen severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has continued to evolve and mutate, emerging lots of viral variants. Several variants have successfully become the predominant strains and spread all over the world because of their ability to evade the pre-existing immunity obtained after previous infections with prototype strain or immunizations. Here, we summarized the prevalence and biological structure of these variants and the efficacy of currently used vaccines against the SARS-CoV-2 variants to provide guidance on how to design vaccines more rationally against the variants.
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Affiliation(s)
| | | | | | | | - Xionglin Fan
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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46
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Tada T, Zhou H, Dcosta BM, Samanovic MI, Mulligan MJ, Landau NR. Partial resistance of SARS-CoV-2 Delta variants to vaccine-elicited antibodies and convalescent sera. iScience 2021; 24:103341. [PMID: 34723159 PMCID: PMC8541826 DOI: 10.1016/j.isci.2021.103341] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 09/13/2021] [Accepted: 10/20/2021] [Indexed: 12/03/2022] Open
Abstract
Highly transmissible SARS-CoV-2 variants identified in India and designated B.1.617, Kappa (B.1.617.1), Delta (B.1.617.2), B.1.618, and B.1.36.29 contain spike mutations L452R, T478K, E484K, E484Q, and N440K located within the spike receptor-binding domain and thus could contribute to increased transmissibility and potentially allow re-infection or cause resistance to vaccine-elicited antibody. To address these issues, we used lentiviruses pseudotyped by variant spikes to measure their neutralization by convalescent sera, vaccine-elicited and Regeneron therapeutic antibodies, and ACE2 affinity. Convalescent sera and vaccine-elicited antibodies neutralized viruses with Delta spike with 2- to 5-fold decrease in titer in different donors. Regeneron antibody cocktail neutralized virus with the Delta spike with a 2.6-fold decrease in titer. Neutralization resistance to serum antibodies and monoclonal antibodies was mediated by L452R mutation. These relatively modest decreases in antibody neutralization titer for viruses with variant spike proteins suggest that current vaccines will remain protective against the family of Delta variants. Vaccine-elicited antibodies neutralize Delta spike with 4- to 5-fold decrease in titer Delta variant is resistant to REGN10933 monoclonal antibody Neutralization resistance is mediated by L452R
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Affiliation(s)
- Takuya Tada
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, New York, NY 10016, USA
| | - Hao Zhou
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, New York, NY 10016, USA
| | - Belinda M Dcosta
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, New York, NY 10016, USA
| | - Marie I Samanovic
- NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Mark J Mulligan
- NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Nathaniel R Landau
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, New York, NY 10016, USA
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47
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Deb P, Molla MMA, Saif-Ur-Rahman KM, Das MC, Das D. A review of epidemiology, clinical features and disease course, transmission dynamics, and neutralization efficacy of SARS-CoV-2 variants. THE EGYPTIAN JOURNAL OF BRONCHOLOGY 2021. [PMCID: PMC8571979 DOI: 10.1186/s43168-021-00090-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background After the first detection in November 2019, SARS-CoV-2 has spread rapidly over the continents and started the pandemic of the millennium. In addition to several novels and repurposed monoclonal antibodies (mAbs) as a therapeutic option against COVID-19, scientists from across the world have developed several candidate vaccines, developed mainly targeting the Wuhan strain, with very promising results to combat this pandemic. Unfortunately like any RNA viruses, SARS CoV-2 has also gone through the accumulation of hundreds and thousands of mutations in their genome lead to the development of several variants of concerns (VOC) and variants of interests (VOI), resulting in increased transmissibility and virulence of the virus, along with their capacity to escape cross-protection. Seemingly, the main hindrance of containing this pandemic right now is the effectiveness of currently available vaccines and mAbs against newly emerging variants. Therefore, it is important to monitor variants epidemiology, transmission dynamics, clinical characteristics, as well as their immune evasion capacity to implement appropriate vaccine strategy and other containment measures. Body In this review, we tried to focus on variants characteristics and to what extent they can escape immunity, provided by both available vaccinated sera and convalescent sera. A stringent literature review was performed using various databases, mentioned in the methodology portion. The current geographical distribution of these variants of SARS CoV-2 has been presented using a heat map. Findings from published articles comparing these variants, in terms of genome epidemiology, transmissibility, viral load dynamics, and association with different waves have been described briefly. Due strength was given while describing variants neutralization potency against current vaccines, mAbs, and also against convalescent sera. Data from both clinical trials and in vitro/ex-vivo studies have been discussed here. Comparative findings from several articles were brought into one concise paper. After careful reviewing of all the available data, it was clear that, without hesitation, we should strengthen our vaccination strategy, because the severity of COVID 19 is reasonably lower, irrespective of variants and vaccine used. Conclusion We hope that many falsified myths and beliefs regarding vaccine immunity and emerging variants will be clarified in light of this available evidence, which we summarized in our paper.
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Lanini S, Capone S, Antinori A, Milleri S, Nicastri E, Camerini R, Agrati C, Castilletti C, Mori F, Sacchi A, Matusali G, Gagliardini R, Ammendola V, Cimini E, Grazioli F, Scorzolini L, Napolitano F, Plazzi MM, Soriani M, De Luca A, Battella S, Sommella A, Contino AM, Barra F, Gentile M, Raggioli A, Shi Y, Girardi E, Maeurer M, Capobianchi MR, Vaia F, Piacentini M, Kroemer G, Vitelli A, Colloca S, Folgori A, Ippolito G, Ottou S, Vita S, Vergori A, D'Abramo A, Petrecchia A, Montaldo C, Scalise E, Grassi G, Casetti R, Bordoni V, Notari S, Colavita F, Meschi S, Lapa D, Bordi L, Murachelli S, Tambasco T, Grillo A, Masone E, Marchioni E, Bardhi D, Porzio O, Cocca F, Murachelli S, Turrini I, Malescio F, Ziviani L, Lawlor R, Poli F, Martire F, Zamboni D, Mazzaferri F. GRAd-COV2, a gorilla adenovirus-based candidate vaccine against COVID-19, is safe and immunogenic in younger and older adults. Sci Transl Med 2021; 14:eabj1996. [PMID: 34698501 DOI: 10.1126/scitranslmed.abj1996] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Simone Lanini
- Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS; 00149, Rome, Italy
| | | | - Andrea Antinori
- Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS; 00149, Rome, Italy
| | - Stefano Milleri
- Centro Ricerche Cliniche di Verona srl; 37134, Verona, Italy
| | - Emanuele Nicastri
- Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS; 00149, Rome, Italy
| | | | - Chiara Agrati
- Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS; 00149, Rome, Italy
| | - Concetta Castilletti
- Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS; 00149, Rome, Italy
| | | | - Alessandra Sacchi
- Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS; 00149, Rome, Italy
| | - Giulia Matusali
- Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS; 00149, Rome, Italy
| | - Roberta Gagliardini
- Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS; 00149, Rome, Italy
| | | | - Eleonora Cimini
- Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS; 00149, Rome, Italy
| | | | - Laura Scorzolini
- Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS; 00149, Rome, Italy
| | | | - Maria M Plazzi
- Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS; 00149, Rome, Italy
| | | | - Aldo De Luca
- Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS; 00149, Rome, Italy
| | | | | | | | | | | | | | - Yufang Shi
- First Affiliated Hospital of Soochow University; Suzhou, 215008, Jiangsu, China.,Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; 200061, Shanghai, China
| | - Enrico Girardi
- Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS; 00149, Rome, Italy
| | - Markus Maeurer
- Division of Immunotherapy, ImmunoSurgery, Champalimaud Foundation; 1400-038, Lisboa, Portugal.,I Medical Clinic, University of Mainz; 55122, Mainz, Germany
| | - Maria R Capobianchi
- Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS; 00149, Rome, Italy.,Saint Camillus International University of Health Sciences, 00131, Rome, Italy
| | - Francesco Vaia
- Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS; 00149, Rome, Italy
| | - Mauro Piacentini
- Department of Biology, University of Rome "Tor Vergata; 00133, Rome, Italy
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, 75006, Paris, France.,Metabolomics and Cell Biology Platforms, Institut Gustave Roussy; 94805, Villejuif, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou; 75015, Paris, France.,Department of Women's and Children's Health, Karolinska University Hospital, 17164, Stockholm, Sweden
| | | | | | | | - Giuseppe Ippolito
- Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS; 00149, Rome, Italy
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Serpeloni JM, Lima Neto QA, Lucio LC, Ramão A, Carvalho de Oliveira J, Gradia DF, Malheiros D, Ferrasa A, Marchi R, Figueiredo DLA, Silva WA, Ribeiro EMSF, Cólus IMS, Cavalli LR. Genome interaction of the virus and the host genes and non-coding RNAs in SARS-CoV-2 infection. Immunobiology 2021; 226:152130. [PMID: 34425415 PMCID: PMC8378551 DOI: 10.1016/j.imbio.2021.152130] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/22/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023]
Abstract
In this review, we highlight the interaction of SARS-CoV-2 virus and host genomes, reporting the current studies on the sequence analysis of SARS-CoV-2 isolates and host genomes from diverse world populations. The main genetic variants that are present in both the virus and host genomes were particularly focused on the ACE2 and TMPRSS2 genes, and their impact on the patients' susceptibility to the virus infection and severity of the disease. Finally, the interaction of the virus and host non-coding RNAs is described in relation to their regulatory roles in target genes and/or signaling pathways critically associated with SARS-CoV-2 infection. Altogether, these studies provide a significant contribution to the knowledge of SARS-CoV-2 mechanisms of infection and COVID-19 pathogenesis. The described genetic variants and molecular factors involved in host/virus genome interactions have significantly contributed to defining patient risk groups, beyond those based on patients' age and comorbidities, and they are promising candidates to be potentially targeted in treatment strategies for COVID-19 and other viral infectious diseases.
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Affiliation(s)
- Juliana M Serpeloni
- Departamento de Biologia Geral, CCB, Universidade Estadual de Londrina, Londrina, PR, Brazil
| | - Quirino Alves Lima Neto
- Departamento de Ciências Básicas da Saúde, CCS, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - Léia Carolina Lucio
- Programa de Pós-graduação em Ciências Aplicadas à Saúde, CCS, Universidade Estadual do Oeste do Paraná, Francisco Beltrão, PR, Brazil
| | - Anelisa Ramão
- Departamento de Ciências Biológicas, Universidade Estadual do Centro-Oeste, Guarapuava, PR, Brazil
| | | | | | - Danielle Malheiros
- Departamento de Genética, SCB, Universidade Federal do Paraná, PR, Brazil
| | - Adriano Ferrasa
- Departamento de Informática, SECATE, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | - Rafael Marchi
- Instituto de Pesquisa Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - David L A Figueiredo
- Departamento de Medicina, Universidade Estadual do Centro-Oeste, UNICENTRO e Instituto de Pesquisa para o Câncer, IPEC, Guarapuava, PR, Brazil
| | - Wilson A Silva
- Departamento de Genética, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, SP, e Instituto de Pesquisa para o Câncer, IPEC, Guarapuava, PR, Brazil
| | | | - Ilce M S Cólus
- Departamento de Biologia Geral, CCB, Universidade Estadual de Londrina, Londrina, PR, Brazil
| | - Luciane R Cavalli
- Instituto de Pesquisa Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil.
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50
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Oude Munnink BB, Worp N, Nieuwenhuijse DF, Sikkema RS, Haagmans B, Fouchier RAM, Koopmans M. The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology. Nat Med 2021; 27:1518-1524. [PMID: 34504335 DOI: 10.1038/s41591-021-01472-w] [Citation(s) in RCA: 139] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/20/2021] [Indexed: 02/08/2023]
Abstract
The current coronavirus disease 2019 (COVID-19) pandemic is the first to apply whole-genome sequencing near to real time, with over 2 million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequences generated and shared through the GISAID platform. This genomic resource informed public health decision-making throughout the pandemic; it also allowed detection of mutations that might affect virulence, pathogenesis, host range or immune escape as well as the effectiveness of SARS-CoV-2 diagnostics and therapeutics. However, genotype-to-phenotype predictions cannot be performed at the rapid pace of genomic sequencing. To prepare for the next phase of the pandemic, a systematic approach is needed to link global genomic surveillance and timely assessment of the phenotypic characteristics of novel variants, which will support the development and updating of diagnostics, vaccines, therapeutics and nonpharmaceutical interventions. This Review summarizes the current knowledge on key viral mutations and variants and looks to the next phase of surveillance of the evolving pandemic.
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Affiliation(s)
- Bas B Oude Munnink
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Nathalie Worp
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - David F Nieuwenhuijse
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Reina S Sikkema
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Bart Haagmans
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands.
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