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Aminiranjbar Z, Gultakti CA, Alangari MN, Wang Y, Demir B, Koker Z, Das AK, Anantram MP, Oren EE, Hihath J. Identifying SARS-CoV-2 Variants Using Single-Molecule Conductance Measurements. ACS Sens 2024; 9:2888-2896. [PMID: 38773960 DOI: 10.1021/acssensors.3c02734] [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: 05/24/2024]
Abstract
The global COVID-19 pandemic has highlighted the need for rapid, reliable, and efficient detection of biological agents and the necessity of tracking changes in genetic material as new SARS-CoV-2 variants emerge. Here, we demonstrate that RNA-based, single-molecule conductance experiments can be used to identify specific variants of SARS-CoV-2. To this end, we (i) select target sequences of interest for specific variants, (ii) utilize single-molecule break junction measurements to obtain conductance histograms for each sequence and its potential mutations, and (iii) employ the XGBoost machine learning classifier to rapidly identify the presence of target molecules in solution with a limited number of conductance traces. This approach allows high-specificity and high-sensitivity detection of RNA target sequences less than 20 base pairs in length by utilizing a complementary DNA probe capable of binding to the specific target. We use this approach to directly detect SARS-CoV-2 variants of concerns B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and B.1.1.529 (Omicron) and further demonstrate that the specific sequence conductance is sensitive to nucleotide mismatches, thus broadening the identification capabilities of the system. Thus, our experimental methodology detects specific SARS-CoV-2 variants, as well as recognizes the emergence of new variants as they arise.
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Affiliation(s)
- Zahra Aminiranjbar
- Department of Electrical and Computer Engineering, University of California Davis, Davis, California 95616, United States
| | - Caglanaz Akin Gultakti
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Mashari Nasser Alangari
- Department of Electrical and Computer Engineering, University of California Davis, Davis, California 95616, United States
- Department of Electrical Engineering, University of Hail, Hail 2240, Saudi Arabia
| | - Yiren Wang
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98115, United States
| | - Busra Demir
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Zeynep Koker
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Arindam K Das
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98115, United States
- Department of Computer Science and Electrical Engineering, Eastern Washington University, Cheney, Washington 99004,United States
| | - M P Anantram
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98115, United States
| | - Ersin Emre Oren
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Joshua Hihath
- Department of Electrical and Computer Engineering, University of California Davis, Davis, California 95616, United States
- Center for Bioelectronics and Biosensors, School of Electrical, Computer, and Energy Engineering, Arizona State University, Phoenix, Arizona 85287, United States
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2
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Yao Z, Zhang L, Duan Y, Tang X, Lu J. Molecular insights into the adaptive evolution of SARS-CoV-2 spike protein. J Infect 2024; 88:106121. [PMID: 38367704 DOI: 10.1016/j.jinf.2024.106121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/02/2024] [Accepted: 02/10/2024] [Indexed: 02/19/2024]
Abstract
The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has substantially damaged the global economy and human health. The spike (S) protein of coronaviruses plays a pivotal role in viral entry by binding to host cell receptors. Additionally, it acts as the primary target for neutralizing antibodies in those infected and is the central focus for currently utilized or researched vaccines. During the virus's adaptation to the human host, the S protein of SARS-CoV-2 has undergone significant evolution. As the COVID-19 pandemic has unfolded, new mutations have arisen and vanished, giving rise to distinctive amino acid profiles within variant of concern strains of SARS-CoV-2. Notably, many of these changes in the S protein have been positively selected, leading to substantial alterations in viral characteristics, such as heightened transmissibility and immune evasion capabilities. This review aims to provide an overview of our current understanding of the structural implications associated with key amino acid changes in the S protein of SARS-CoV-2. These research findings shed light on the intricate and dynamic nature of viral evolution, underscoring the importance of continuous monitoring and analysis of viral genomes. Through these molecular-level investigations, we can attain deeper insights into the virus's adaptive evolution, offering valuable guidance for designing vaccines and developing antiviral drugs to combat the ever-evolving viral threats.
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Affiliation(s)
- Zhuocheng Yao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lin Zhang
- College of Fishery, Ocean University of China, Qingdao 266003, China
| | - Yuange Duan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
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3
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Bi W, Tang K, Chen G, Xie Y, Polizzi NF, DeGrado WF, Yuan S, Dang B. An enhanced broad-spectrum peptide inhibits Omicron variants in vivo. Cell Rep Med 2024; 5:101418. [PMID: 38340726 PMCID: PMC10897629 DOI: 10.1016/j.xcrm.2024.101418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 11/29/2023] [Accepted: 01/17/2024] [Indexed: 02/12/2024]
Abstract
The continual emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) poses a major challenge to vaccines and antiviral therapeutics due to their extensive evasion of immunity. Aiming to develop potent and broad-spectrum anticoronavirus inhibitors, we generated A1-(GGGGS)7-HR2m (A1L35HR2m) by introducing an angiotensin-converting enzyme 2 (ACE2)-derived peptide A1 to the N terminus of the viral HR2-derived peptide HR2m through a long flexible linker, which showed significantly improved antiviral activity. Further cholesterol (Chol) modification at the C terminus of A1L35HR2m greatly enhanced the inhibitory activities against SARS-CoV-2, SARS-CoV-2 VOCs, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV) pseudoviruses, with IC50 values ranging from 0.16 to 5.53 nM. A1L35HR2m-Chol also potently inhibits spike-protein-mediated cell-cell fusion and the replication of authentic Omicron BA.2.12.1, BA.5, and EG.5.1. Importantly, A1L35HR2m-Chol distributed widely in respiratory tract tissue and had a long half-life (>10 h) in vivo. Intranasal administration of A1L35HR2m-Chol to K18-hACE2 transgenic mice potently inhibited Omicron BA.5 and EG.5.1 infection both prophylactically and therapeutically.
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Affiliation(s)
- Wenwen Bi
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, Zhejiang, China; Frontier Biotechnology Laboratory, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310030, China.
| | - Kaiming Tang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China; State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Guilin Chen
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310030, China
| | - Yubin Xie
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China; State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Nicholas F Polizzi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Shuofeng Yuan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China; State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Bobo Dang
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310030, China.
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4
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Thimmiraju SR, Kimata JT, Pollet J. Pseudoviruses, a safer toolbox for vaccine development against enveloped viruses. Expert Rev Vaccines 2024; 23:174-185. [PMID: 38164690 DOI: 10.1080/14760584.2023.2299380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
INTRODUCTION Pseudoviruses are recombinant, replication-incompetent, viral particles designed to mimic the surface characteristics of native enveloped viruses. They are a safer, and cost-effective research alternative to live viruses. With the potential emergence of the next major infectious disease, more vaccine scientists must become familiar with the pseudovirus platform as a vaccine development tool to mitigate future outbreaks. AREAS COVERED This review aims at vaccine developers to provide a basic understanding of pseudoviruses, list their production methods, and discuss their utility to assess vaccine efficacy against enveloped viral pathogens. We further illustrate their usefulness as wet-lab simulators for emerging mutant variants, and new viruses to help prepare for current and future viral outbreaks, minimizing the need for gain-of-function experiments with highly infectious or lethal enveloped viruses. EXPERT OPINION With this platform, researchers can better understand the role of virus-receptor interactions and entry in infections, prepare for dangerous mutations, and develop effective vaccines.
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Affiliation(s)
- Syamala R Thimmiraju
- Department of Pediatrics, Section of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital Center for Vaccine Development, Baylor College of Medicine, Houston, TX, USA
| | - Jason T Kimata
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Jeroen Pollet
- Department of Pediatrics, Section of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital Center for Vaccine Development, Baylor College of Medicine, Houston, TX, USA
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5
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Kistler KE, Bedford T. An atlas of continuous adaptive evolution in endemic human viruses. Cell Host Microbe 2023; 31:1898-1909.e3. [PMID: 37883977 DOI: 10.1016/j.chom.2023.09.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/25/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]
Abstract
Through antigenic evolution, viruses such as seasonal influenza evade recognition by neutralizing antibodies. This means that a person with antibodies well tuned to an initial infection will not be protected against the same virus years later and that vaccine-mediated protection will decay. To expand our understanding of which endemic human viruses evolve in this fashion, we assess adaptive evolution across the genome of 28 endemic viruses spanning a wide range of viral families and transmission modes. Surface proteins consistently show the highest rates of adaptation, and ten viruses in this panel are estimated to undergo antigenic evolution to selectively fix mutations that enable the escape of prior immunity. Thus, antibody evasion is not an uncommon evolutionary strategy among human viruses, and monitoring this evolution will inform future vaccine efforts. Additionally, by comparing overall amino acid substitution rates, we show that SARS-CoV-2 is accumulating protein-coding changes at substantially faster rates than endemic viruses.
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Affiliation(s)
- Kathryn E Kistler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA.
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA
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6
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Sevilya Z, Kuzmina A, Cipok M, Hershkovitz V, Keidar-Friedman D, Taube R, Lev EI. Differential platelet activation through an interaction with spike proteins of different SARS-CoV-2 variants. J Thromb Thrombolysis 2023; 56:538-547. [PMID: 37736784 DOI: 10.1007/s11239-023-02891-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/23/2023] [Indexed: 09/23/2023]
Abstract
COVID-19 disease is associated with an increased risk of thrombotic complications, which contribute to high short-term mortality. Patients with COVID-19 demonstrate enhanced platelet turnover and reactivity, which may have a role in the development of thrombotic events and disease severity. Evidence has suggested direct interaction between SARS-CoV-2 and platelets, resulting in platelets activation. Here, we compare the effect of various SARS-CoV-2 spike variants on platelet activation. Engineered lentiviral particles were pseudotyped with spike SARS-CoV-2 variants and incubated with Platelet Rich Plasma obtained from healthy individuals. The pseudotyped SARS-CoV-2 exhibiting the wild-type Wuhan-Hu spike protein stimulated platelets to increase expression of the surface CD62P and activated αIIbβ3 markers by 3.5 ± 1.2 and 3.3 ± 0.7 fold, respectively (P = 0.004 and 0.003). The Delta variant induced much higher levels of platelet activation; CD62P expression was increased by 6.6 ± 2.2 fold and activated αIIbβ3 expression was increased by 5.0 ± 1.5 fold (P = 0.005 and 0.026, respectively). The Omicron BA.1 and the Alpha variants induced the lowest level of activation; CD62P expression was increased by 1.7 ± 0.4 and 1.6 ± 0.9 fold, respectively (P = 0.003 and 0.008), and activated αIIbβ3 expression by 1.8 ± 1.1 and 1.6 ± 0.8, respectively (P = 0.003 and 0.001). The Omicron BA.2 variant induced an increase of platelets activation comparable to the Wuhan-Hu (2.8 ± 1.2 and 2.1 ± 1.3 fold for CD62P and activated αIIbβ3 markers, respectively). The results obtained for various COVID-19 variants are in correlation with the clinical severity and mortality reported for these variants.
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Affiliation(s)
- Ziv Sevilya
- Cardiology Department, Assuta Ashdod Medical Center, Ashdod, Israel.
| | - Alona Kuzmina
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Michal Cipok
- Hematology Laboratory, Assuta Ashdod Medical Center, Ashdod, Israel
| | - Vera Hershkovitz
- Hematology Laboratory, Assuta Ashdod Medical Center, Ashdod, Israel
| | | | - Ran Taube
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Eli I Lev
- Cardiology Department, Assuta Ashdod Medical Center, Ashdod, Israel
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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Xing M, Wang Y, Wang X, Liu J, Dai W, Hu G, He F, Zhao Q, Li Y, Sun L, Wang Y, Du S, Dong Z, Pang C, Hu Z, Zhang X, Xu J, Cai Q, Zhou D. Broad-spectrum vaccine via combined immunization routes triggers potent immunity to SARS-CoV-2 and its variants. J Virol 2023; 97:e0072423. [PMID: 37706688 PMCID: PMC10617383 DOI: 10.1128/jvi.00724-23] [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: 05/16/2023] [Accepted: 07/09/2023] [Indexed: 09/15/2023] Open
Abstract
IMPORTANCE The development of broad-spectrum SARS-CoV-2 vaccines will reduce the global economic and public health stress from the COVID-19 pandemic. The use of conserved T-cell epitopes in combination with spike antigen that induce humoral and cellular immune responses simultaneously may be a promising strategy to further enhance the broad spectrum of COVID-19 vaccine candidates. Moreover, this research suggests that the combined vaccination strategies have the ability to induce both effective systemic and mucosal immunity, which may represent promising strategies for maximizing the protective efficacy of respiratory virus vaccines.
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Affiliation(s)
- Man Xing
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yihan Wang
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xinyu Wang
- MOE&NHC&CAMS Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infections Disease and Biosecurity, Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiaojiao Liu
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Weiqian Dai
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Gaowei Hu
- MOE&NHC&CAMS Key Laboratory of Medical Molecular, Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Furong He
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Qian Zhao
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ying Li
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Lingjin Sun
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yuyan Wang
- MOE&NHC&CAMS Key Laboratory of Medical Molecular, Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shujuan Du
- MOE&NHC&CAMS Key Laboratory of Medical Molecular, Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhongwei Dong
- MOE&NHC&CAMS Key Laboratory of Medical Molecular, Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chongjie Pang
- Department of Infectious Diseases, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhidong Hu
- Department of Clinical Laboratory, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiaoyan Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jianqing Xu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Qiliang Cai
- MOE&NHC&CAMS Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infections Disease and Biosecurity, Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Dongming Zhou
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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8
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Das A, Pathak S, Premkumar M, Sarpparajan CV, Balaji ER, Duttaroy AK, Banerjee A. A brief overview of SARS-CoV-2 infection and its management strategies: a recent update. Mol Cell Biochem 2023:10.1007/s11010-023-04848-3. [PMID: 37742314 DOI: 10.1007/s11010-023-04848-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/02/2023] [Indexed: 09/26/2023]
Abstract
The COVID-19 pandemic has become a global health crisis, inflicting substantial morbidity and mortality worldwide. A diverse range of symptoms, including fever, cough, dyspnea, and fatigue, characterizes COVID-19. A cytokine surge can exacerbate the disease's severity. This phenomenon involves an increased immune response, marked by the excessive release of inflammatory cytokines like IL-6, IL-8, TNF-α, and IFNγ, leading to tissue damage and organ dysfunction. Efforts to reduce the cytokine surge and its associated complications have garnered significant attention. Standardized management protocols have incorporated treatment strategies, with corticosteroids, chloroquine, and intravenous immunoglobulin taking the forefront. The recent therapeutic intervention has also assisted in novel strategies like repurposing existing medications and the utilization of in vitro drug screening methods to choose effective molecules against viral infections. Beyond acute management, the significance of comprehensive post-COVID-19 management strategies, like remedial measures including nutritional guidance, multidisciplinary care, and follow-up, has become increasingly evident. As the understanding of COVID-19 pathogenesis deepens, it is becoming increasingly evident that a tailored approach to therapy is imperative. This review focuses on effective treatment measures aimed at mitigating COVID-19 severity and highlights the significance of comprehensive COVID-19 management strategies that show promise in the battle against COVID-19.
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Affiliation(s)
- Alakesh Das
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai, Tamil Nadu, 603103, India
| | - Surajit Pathak
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai, Tamil Nadu, 603103, India
| | - Madhavi Premkumar
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai, Tamil Nadu, 603103, India
| | - Chitra Veena Sarpparajan
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai, Tamil Nadu, 603103, India
| | - Esther Raichel Balaji
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai, Tamil Nadu, 603103, India
| | - Asim K Duttaroy
- Department of Nutrition, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
| | - Antara Banerjee
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai, Tamil Nadu, 603103, India.
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9
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Frische A, Gunalan V, Krogfelt KA, Fomsgaard A, Lassaunière R. A Candidate DNA Vaccine Encoding the Native SARS-CoV-2 Spike Protein Induces Anti-Subdomain 1 Antibodies. Vaccines (Basel) 2023; 11:1451. [PMID: 37766128 PMCID: PMC10535225 DOI: 10.3390/vaccines11091451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/25/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
The ideal vaccine against viral infections should elicit antibody responses that protect against divergent strains. Designing broadly protective vaccines against SARS-CoV-2 and other divergent viruses requires insight into the specific targets of cross-protective antibodies on the viral surface protein(s). However, unlike therapeutic monoclonal antibodies, the B-cell epitopes of vaccine-induced polyclonal antibody responses remain poorly defined. Here we show that, through the combination of neutralizing antibody functional responses with B-cell epitope mapping, it is possible to identify unique antibody targets associated with neutralization breadth. The polyclonal antibody profiles of SARS-CoV-2 index-strain-vaccinated rabbits that demonstrated a low, intermediate, or high neutralization efficiency of different SARS-CoV-2 variants of concern (VOCs) were distinctly different. Animals with an intermediate and high cross-neutralization of VOCs targeted fewer antigenic sites on the spike protein and targeted one particular epitope, subdomain 1 (SD1), situated outside the receptor binding domain (RBD). Our results indicate that a targeted functional antibody response and an additional focus on non-RBD epitopes could be effective for broad protection against different SARS-CoV-2 variants. We anticipate that the approach taken in this study can be applied to other viral vaccines for identifying future epitopes that confer cross-neutralizing antibody responses, and that our findings will inform a rational vaccine design for SARS-CoV-2.
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Affiliation(s)
- Anders Frische
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen, Denmark; (A.F.); (V.G.); (K.A.K.); (A.F.)
- Section of Molecular and Medicinal Biology, Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
| | - Vithiagaran Gunalan
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen, Denmark; (A.F.); (V.G.); (K.A.K.); (A.F.)
| | - Karen Angeliki Krogfelt
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen, Denmark; (A.F.); (V.G.); (K.A.K.); (A.F.)
- Section of Molecular and Medicinal Biology, Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
| | - Anders Fomsgaard
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen, Denmark; (A.F.); (V.G.); (K.A.K.); (A.F.)
- Infectious Diseases Unit, Clinical Institute, University of Southern Denmark, 5230 Odense, Denmark
| | - Ria Lassaunière
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen, Denmark; (A.F.); (V.G.); (K.A.K.); (A.F.)
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10
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Neary M, Sharp J, Gallardo-Toledo E, Herriott J, Kijak E, Bramwell C, Cox H, Tatham L, Box H, Curley P, Arshad U, Rajoli RKR, Pertinez H, Valentijn A, Dhaliwal K, Mc Caughan F, Hobson J, Rannard S, Kipar A, Stewart JP, Owen A. Evaluation of Nafamostat as Chemoprophylaxis for SARS-CoV-2 Infection in Hamsters. Viruses 2023; 15:1744. [PMID: 37632086 PMCID: PMC10458615 DOI: 10.3390/v15081744] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
The successful development of a chemoprophylaxis against SARS-CoV-2 could provide a tool for infection prevention that is implementable alongside vaccination programmes. Nafamostat is a serine protease inhibitor that inhibits SARS-CoV-2 entry in vitro, but it has not been characterised for chemoprophylaxis in animal models. Clinically, nafamostat is limited to intravenous delivery and has an extremely short plasma half-life. This study sought to determine whether intranasal dosing of nafamostat at 5 mg/kg twice daily was able to prevent the airborne transmission of SARS-CoV-2 from infected to uninfected Syrian Golden hamsters. SARS-CoV-2 RNA was detectable in the throat swabs of the water-treated control group 4 days after cohabitation with a SARS-CoV-2 inoculated hamster. However, throat swabs from the intranasal nafamostat-treated hamsters remained SARS-CoV-2 RNA negative for the full 4 days of cohabitation. Significantly lower SARS-CoV-2 RNA concentrations were seen in the nasal turbinates of the nafamostat-treated group compared to the control (p = 0.001). A plaque assay quantified a significantly lower concentration of infectious SARS-CoV-2 in the lungs of the nafamostat-treated group compared to the control (p = 0.035). When taken collectively with the pathological changes observed in the lungs and nasal mucosa, these data are strongly supportive of the utility of intranasally delivered nafamostat for the prevention of SARS-CoV-2 infection.
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Affiliation(s)
- Megan Neary
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L3 5TR, UK (J.S.); (E.G.-T.); (E.K.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L3 5TR, UK
| | - Joanne Sharp
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L3 5TR, UK (J.S.); (E.G.-T.); (E.K.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L3 5TR, UK
| | - Eduardo Gallardo-Toledo
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L3 5TR, UK (J.S.); (E.G.-T.); (E.K.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L3 5TR, UK
| | - Joanne Herriott
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L3 5TR, UK (J.S.); (E.G.-T.); (E.K.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L3 5TR, UK
| | - Edyta Kijak
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L3 5TR, UK (J.S.); (E.G.-T.); (E.K.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L3 5TR, UK
| | - Chloe Bramwell
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L3 5TR, UK (J.S.); (E.G.-T.); (E.K.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L3 5TR, UK
| | - Helen Cox
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L3 5TR, UK (J.S.); (E.G.-T.); (E.K.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L3 5TR, UK
| | - Lee Tatham
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L3 5TR, UK (J.S.); (E.G.-T.); (E.K.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L3 5TR, UK
| | - Helen Box
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L3 5TR, UK (J.S.); (E.G.-T.); (E.K.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L3 5TR, UK
| | - Paul Curley
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L3 5TR, UK (J.S.); (E.G.-T.); (E.K.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L3 5TR, UK
| | - Usman Arshad
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L3 5TR, UK (J.S.); (E.G.-T.); (E.K.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L3 5TR, UK
| | - Rajith K. R. Rajoli
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L3 5TR, UK (J.S.); (E.G.-T.); (E.K.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L3 5TR, UK
| | - Henry Pertinez
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L3 5TR, UK (J.S.); (E.G.-T.); (E.K.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L3 5TR, UK
| | - Anthony Valentijn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L3 5TR, UK (J.S.); (E.G.-T.); (E.K.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L3 5TR, UK
| | - Kevin Dhaliwal
- Translational Healthcare Technologies Group, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH10 5HF, UK
| | - Frank Mc Caughan
- Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Papworth Road, Cambridge CB2 1BN, UK
| | - James Hobson
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L3 5TR, UK
| | - Steve Rannard
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L3 5TR, UK
| | - Anja Kipar
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 5TR, UK; (A.K.)
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - James P. Stewart
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 5TR, UK; (A.K.)
| | - Andrew Owen
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L3 5TR, UK (J.S.); (E.G.-T.); (E.K.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L3 5TR, UK
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11
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Knell AI, Böhm AK, Jäger M, Kerschbaum J, Engl S, Rudnicki M, Buchwinkler L, Bellmann-Weiler R, Posch W, Weiss G. Virus-Subtype-Specific Cellular and Humoral Immune Response to a COVID-19 mRNA Vaccine in Chronic Kidney Disease Patients and Renal Transplant Recipients. Microorganisms 2023; 11:1756. [PMID: 37512928 PMCID: PMC10383116 DOI: 10.3390/microorganisms11071756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Patients with chronic kidney disease (CKD) or immunosuppression are at increased risk of severe SARS-CoV-2 infection. The vaccination of CKD patients has resulted in lower antibody concentrations and possibly reduced protection. However, little information is available on how T-cell-mediated immune response is affected in those patients and how vaccine-induced immune responses can neutralise different SARS-CoV-2 variants. Herein, we studied virus-specific humoral and cellular immune responses after two doses of mRNA-1273 (Moderna) vaccine in 42 patients suffering from CKD, small vessel vasculitis (maintenance phase), or kidney transplant recipients (KT). Serum and PBMCs from baseline and at three months after vaccination were used to determine SARS-CoV-2 S1-specific antibodies, neutralisation titers against SARS-CoV-2 WT, B1.617.2 (delta), and BA.1 (omicron) variants as well as virus-specific T-cells via IFNγ ELISpot assays. We observed a significant increase in quantitative and neutralising antibody titers against SARS-CoV-2 and significantly increased T-cell responses to SARS-CoV-2 S1 antigen after vaccination only in the CKD patients. In patients with vasculitis, neither humoral nor cellular responses were detected. In KT recipients, antibodies and virus neutralisation against WT and delta, but not against omicron BA.1, was assured. Importantly, we found no specific SARS-CoV-2 T-cell response in vasculitis and KT subjects, although unspecific T-cell activation was evident in most patients even before vaccination. While pre-dialysis CKD patients appear to mount an effective immune response for in vitro neutralisation of SARS-CoV-2, KT and vasculitis patients under immunosuppressive therapy were insufficiently protected from SARS-CoV-2 two months after the second dose of an mRNA vaccine.
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Affiliation(s)
- Astrid I Knell
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Anna K Böhm
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Michael Jäger
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, 6020 Innsbruck, Austria
| | - Julia Kerschbaum
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Sabine Engl
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Michael Rudnicki
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Lukas Buchwinkler
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Rosa Bellmann-Weiler
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Wilfried Posch
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, 6020 Innsbruck, Austria
| | - Günter Weiss
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
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12
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Hernández-Bello J, Sierra-García-de-Quevedo JJ, Morales-Núñez JJ, Santoscoy-Ascencio G, Díaz-Pérez SA, Gutiérrez-Brito JA, Muñoz-Valle JF. BNT162b2 Vaccination after SARS-CoV-2 Infection Changes the Dynamics of Total and Neutralizing Antibodies against SARS-CoV-2: A 6-Month Prospective Cohort Study. Vaccines (Basel) 2023; 11:1127. [PMID: 37376516 DOI: 10.3390/vaccines11061127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/07/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
This study aimed to analyze the dynamics, duration, and production of total and neutralizing antibodies induced by the BNT162b2 vaccine and the possible effect of gender and prior SARS-CoV-2 infection on the generation of these antibodies. Total antibodies were quantified via chemiluminescent microparticle immunoassay (CMIA), and neutralizing antibodies were quantified using the cPass SARS-CoV-2 kit. Individuals with a history of COVID-19 produced twice as many antibodies than vaccinated individuals without prior SARS-CoV-2 infection, with an exponential increase observed in just six days. In those without a COVID-19 history, similar antibody production was reached 45 days after vaccination. Although total antibodies decline considerably in the first two months, the neutralizing antibodies and their inhibitory capacity (>96%) persist up to 6 months after the first dose. There was a tendency for higher total antibodies in women than men, but not at the inhibition capacity level. We suggest that the decline in total antibodies should not be considered as an indicator of loss of protective immunity because most antibodies decay two months after the second dose, but neutralizing antibodies remain constant for at least six months. Therefore, these latter antibodies could be better indicators for estimating the time-dependent vaccine efficacy.
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Affiliation(s)
- Jorge Hernández-Bello
- Institute of Research in Biomedical Sciences, University Center of Health Sciences (CUCS), University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | | | - José Javier Morales-Núñez
- Institute of Research in Biomedical Sciences, University Center of Health Sciences (CUCS), University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | | | - Saúl Alberto Díaz-Pérez
- Institute of Research in Biomedical Sciences, University Center of Health Sciences (CUCS), University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Jesús Alberto Gutiérrez-Brito
- Institute of Research in Biomedical Sciences, University Center of Health Sciences (CUCS), University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - José Francisco Muñoz-Valle
- Institute of Research in Biomedical Sciences, University Center of Health Sciences (CUCS), University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
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13
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Kuzmina A, Korovin D, Cohen Lass I, Atari N, Ottolenghi A, Hu P, Mandelboim M, Rosental B, Rosenberg E, Diaz-Griffero F, Taube R. Changes within the P681 residue of spike dictate cell fusion and syncytia formation of Delta and Omicron variants of SARS-CoV-2 with no effects on neutralization or infectivity. Heliyon 2023; 9:e16750. [PMID: 37292300 PMCID: PMC10238279 DOI: 10.1016/j.heliyon.2023.e16750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 04/13/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023] Open
Abstract
The rapid spread and dominance of the Omicron SARS-CoV-2 lineages have posed severe health challenges worldwide. While extensive research on the role of the Receptor Binding Domain (RBD) in promoting viral infectivity and vaccine sensitivity has been well documented, the functional significance of the 681PRRAR/SV687 polybasic motif of the viral spike is less clear. In this work, we monitored the infectivity levels and neutralization potential of the wild-type human coronavirus 2019 (hCoV-19), Delta, and Omicron SARS-CoV-2 pseudoviruses against sera samples drawn four months post administration of a third dose of the BNT162b2 mRNA vaccine. Our findings show that in comparison to hCoV-19 and Delta SARS-CoV-2, Omicron lineages BA.1 and BA.2 exhibit enhanced infectivity and a sharp decline in their sensitivity to vaccine-induced neutralizing antibodies. Interestingly, P681 mutations within the viral spike do not play a role in the neutralization potential or infectivity of SARS Cov-2 pseudoviruses carrying mutations in this position. The P681 residue however, dictates the ability of the spike protein to promote fusion and syncytia formation between infected cells. While spike from hCoV-19 (P681) and Omicron (H681) promote only modest cell fusion and formation of syncytia between cells that express the spike-protein, Delta spike (R681) displays enhanced fusogenic activity and promotes syncytia formation. Additional analysis shows that a single P681R mutation within the hCoV-19 spike, or H681R within the Omicron spike, restores fusion potential to similar levels observed for the Delta R681 spike. Conversely, R681P point mutation within the spike of Delta pseudovirus abolishes efficient fusion and syncytia formation. Our investigation also demonstrates that spike proteins from hCoV-19 and Delta SARS-CoV-2 are efficiently incorporated into viral particles relative to the spike of Omicron lineages. We conclude that the third dose of the Pfizer-BNT162b2 provides appreciable protection against the newly emerged Omicron sub-lineages. However, the neutralization sensitivity of these new variants is diminished relative to that of the hCoV-19 or Delta SARS-CoV-2. We further show that the P681 residue within spike dictates cell fusion and syncytia formation with no effects on the infectivity of the specific viral variant and on its sensitivity to vaccine-mediated neutralization.
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Affiliation(s)
- Alona Kuzmina
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
| | - Dina Korovin
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
| | - Ido Cohen Lass
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
| | - Nofar Atari
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel-Hashomer, Israel
| | - Aner Ottolenghi
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
- Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Israel
| | - Pan Hu
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michal Mandelboim
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel-Hashomer, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv, Israel
| | - Benyamin Rosental
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
- Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Israel
| | | | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ran Taube
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
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14
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Wouters E, Verbrugghe C, Abdelnabi R, Devloo R, De Clippel D, Jochmans D, De Bleser D, Weynand B, Compernolle V, Neyts J, Feys HB. Intranasal administration of convalescent plasma protects against SARS-CoV-2 infection in hamsters. EBioMedicine 2023; 92:104597. [PMID: 37148586 PMCID: PMC10171892 DOI: 10.1016/j.ebiom.2023.104597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/18/2023] [Accepted: 04/18/2023] [Indexed: 05/08/2023] Open
Abstract
BACKGROUND Convalescent plasma (CP) transfusion is an early option for treating infections with pandemic potential, often preceding vaccine or antiviral drug rollout. Heterogenous findings from randomized clinical trials on transfusion of COVID-19 CP (CCP) have been reported. However, meta-analysis suggests that transfusion of high titer CCP is associated with a mortality benefit for COVID-19 outpatients or inpatients treated within 5 days after symptom onset, indicating the importance of early administration. METHODS We tested if CCP is an effective prophylactic against SARS-CoV-2 infection by the intranasal administration of 25 μL CCP/nostril (i.e. 0.01-0.06 mg anti-RBD antibodies/kg) in hamsters exposed to infected littermates. FINDINGS In this model, 40% of CCP treated hamsters were fully protected and 40% had significantly reduced viral loads, the remaining 20% was not protected. The effect seems dose-dependent because high-titer CCP from a vaccinated donor was more effective than low-titer CCP from a donation prior to vaccine rollout. Intranasal administration of human CCP resulted in a reactive (immune) response in hamster lungs, however this was not observed upon administration of hamster CCP. INTERPRETATION We conclude that CCP is an effective prophylactic when used directly at the site of primary infection. This option should be considered in future prepandemic preparedness plans. FUNDING Flanders Innovation & Entrepreneurship (VLAIO) and the Foundation for Scientific Research of the Belgian Red Cross Flanders.
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Affiliation(s)
- Elise Wouters
- Transfusion Research Center, Belgian Red Cross-Flanders, Ghent, Belgium
| | - Caro Verbrugghe
- Transfusion Research Center, Belgian Red Cross-Flanders, Ghent, Belgium; Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Rana Abdelnabi
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000, Leuven, Belgium
| | - Rosalie Devloo
- Transfusion Research Center, Belgian Red Cross-Flanders, Ghent, Belgium
| | | | - Dirk Jochmans
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000, Leuven, Belgium
| | | | - Birgit Weynand
- KU Leuven Department of Imaging and Pathology, Translational Cell and Tissue Research, Division of Translational Cell and Tissue Research, B-3000, Leuven, Belgium
| | - Veerle Compernolle
- Transfusion Research Center, Belgian Red Cross-Flanders, Ghent, Belgium; Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Blood Services of the Belgian Red Cross-Flanders, Mechelen, Belgium; Transfusion Innovation Center, Belgian Red Cross-Flanders, Ghent, Belgium
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000, Leuven, Belgium
| | - Hendrik B Feys
- Transfusion Research Center, Belgian Red Cross-Flanders, Ghent, Belgium; Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Blood Services of the Belgian Red Cross-Flanders, Mechelen, Belgium.
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15
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Liu X, Chen Y, Li X, Li J. Global stability of latency-age/stage-structured epidemic models with differential infectivity. J Math Biol 2023; 86:80. [PMID: 37093296 PMCID: PMC10123597 DOI: 10.1007/s00285-023-01918-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 04/02/2023] [Accepted: 04/03/2023] [Indexed: 04/25/2023]
Abstract
In this paper, we first formulate a system of ODEs-PDE to model diseases with latency-age and differential infectivity. Then, based on the ways how latent individuals leave the latent stage, one ODE and two DDE models are derived. We only focus on the global stability of the models. All the models have some similarities in the existence of equilibria. Each model has a threshold dynamics for global stability, which is completely characterized by the basic reproduction number. The approach is the Lyapunov direct method. We propose an idea on constructing Lyapunov functionals for the two DDE and the original ODEs-PDE models. During verifying the negative (semi-)definiteness of derivatives of the Lyapunov functionals along solutions, a novel positive definite function and a new inequality are used. The idea here is also helpful in applying the Lyapunov direct method to prove the global stability of some epidemic models with age structure or delays.
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Affiliation(s)
- Xiaogang Liu
- Xi'an Key Laboratory of Human-Machine Integration and Control Technology for Intelligent Rehabilitation, Xijing University, No. 1, Xijing Road, Xi'an, 710123, Shaanxi, China
| | - Yuming Chen
- Department of Mathematics, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, N2L 3C5, Canada
| | - Xiaomin Li
- Xi'an Key Laboratory of Human-Machine Integration and Control Technology for Intelligent Rehabilitation, Xijing University, No. 1, Xijing Road, Xi'an, 710123, Shaanxi, China
| | - Jianquan Li
- Xi'an Key Laboratory of Human-Machine Integration and Control Technology for Intelligent Rehabilitation, Xijing University, No. 1, Xijing Road, Xi'an, 710123, Shaanxi, China.
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16
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He X, He C, Hong W, Yang J, Wei X. Research progress in spike mutations of SARS-CoV-2 variants and vaccine development. Med Res Rev 2023. [PMID: 36929527 DOI: 10.1002/med.21941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 09/27/2022] [Accepted: 02/26/2023] [Indexed: 03/18/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic can hardly end with the emergence of different variants over time. In the past 2 years, several variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), such as the Delta and Omicron variants, have emerged with higher transmissibility, immune evasion and drug resistance, leading to higher morbidity and mortality in the population. The prevalent variants of concern (VOCs) share several mutations on the spike that can affect virus characteristics, including transmissibility, antigenicity, and immune evasion. Increasing evidence has demonstrated that the neutralization capacity of sera from COVID-19 convalescent or vaccinated individuals is decreased against SARS-CoV-2 variants. Moreover, the vaccine effectiveness of current COVID-19 vaccines against SARS-CoV-2 VOCs is not as high as that against wild-type SARS-CoV-2. Therefore, more attention might be paid to how the mutations impact vaccine effectiveness. In this review, we summarized the current studies on the mutations of the SARS-CoV-2 spike, particularly of the receptor binding domain, to elaborate on how the mutations impact the infectivity, transmissibility and immune evasion of the virus. The effects of mutations in the SARS-CoV-2 spike on the current therapeutics were highlighted, and potential strategies for future vaccine development were suggested.
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Affiliation(s)
- Xuemei He
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Cai He
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Weiqi Hong
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jingyun Yang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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17
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Zhu Y, Li M, Liu N, Wu T, Han X, Zhao G, He Y. Development of highly effective LCB1-based lipopeptides targeting the spike receptor-binding motif of SARS-CoV-2. Antiviral Res 2023; 211:105541. [PMID: 36682464 PMCID: PMC9851916 DOI: 10.1016/j.antiviral.2023.105541] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/07/2023] [Accepted: 01/12/2023] [Indexed: 01/21/2023]
Abstract
LCB1 is a computationally designed 56-mer miniprotein targeting the spike (S) receptor-binding motif of SARS-CoV- 2 with high potent activity (Science, 2020; Cell host microbe, 2021); however, recent studies have demonstrated that emerging SARS-CoV-2 variants are highly resistant to LCB1's inhibition. In this study, we first identified a truncated peptide termed LCB1v8, which maintained the high antiviral potency. Then, a group of lipopeptides were generated by modifying LCB1v8 with diverse lipids, and of two lipopeptides, the C-terminally stearicacid-conjugtaed LCB1v17 and cholesterol-conjugated LCB1v18, were highly effective in inhibiting both S protein-pseudovirus and authentic SARS-CoV-2 infections. We further showed that LCB1-based inhibitors had similar α-helicity and thermostability in structure and bound to the target-mimic RBD protein with high affinity, and the lipopeptides exhibited greatly enhanced binding with the viral and cellular membranes, improved inhibitory activities against emerging SARS-CoV-2 variants. Moreover, LCB1v18 was validated with high preventive and therapeutic efficacies in K18-hACE2 transgenic mice against lethal SARS-CoV-2 challenge. In conclusion, our studies have provided important information for understanding the structure and activity relationship (SAR) of LCB1 inhibitor and would guide the future development of novel antivirals.
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Affiliation(s)
- Yuanmei Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Min Li
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Nian Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Tong Wu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xuelian Han
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Guangyu Zhao
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China.
| | - Yuxian He
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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18
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Kumar K, Tan WS, Arshad SS, Ho KL. Virus-like Particles of Nodavirus Displaying the Receptor Binding Domain of SARS-CoV-2 Spike Protein: A Potential VLP-Based COVID-19 Vaccine. Int J Mol Sci 2023; 24:ijms24054398. [PMID: 36901827 PMCID: PMC10001971 DOI: 10.3390/ijms24054398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/06/2023] [Accepted: 02/19/2023] [Indexed: 02/25/2023] Open
Abstract
Since the outbreak of the coronavirus disease 2019 (COVID-19), various vaccines have been developed for emergency use. The efficacy of the initial vaccines based on the ancestral strain of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) has become a point of contention due to the emergence of new variants of concern (VOCs). Therefore, continuous innovation of new vaccines is required to target upcoming VOCs. The receptor binding domain (RBD) of the virus spike (S) glycoprotein has been extensively used in vaccine development due to its role in host cell attachment and penetration. In this study, the RBDs of the Beta (β) and Delta (δ) variants were fused to the truncated Macrobrachium rosenbergii nodavirus capsid protein without the protruding domain (CΔ116-MrNV-CP). Immunization of BALB/c mice with the virus-like particles (VLPs) self-assembled from the recombinant CP showed that, with AddaVax as an adjuvant, a significantly high level of humoral response was elicited. Specifically, mice injected with equimolar of adjuvanted CΔ116-MrNV-CP fused with the RBD of the β- and δ-variants increased T helper (Th) cell production with a CD8+/CD4+ ratio of 0.42. This formulation also induced proliferation of macrophages and lymphocytes. Overall, this study demonstrated that the nodavirus truncated CP fused with the SARS-CoV-2 RBD has potential to be developed as a VLP-based COVID-19 vaccine.
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Affiliation(s)
- Kiven Kumar
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia
| | - Wen Siang Tan
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia
| | - Siti Suri Arshad
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia
- Correspondence: ; Tel.: +603-9769-2729
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19
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Santos da Silva E, Servais JY, Kohnen M, Arendt V, Gilson G, Staub T, Seguin-Devaux C, Perez-Bercoff D. Vaccine- and Breakthrough Infection-Elicited Pre-Omicron Immunity More Effectively Neutralizes Omicron BA.1, BA.2, BA.4 and BA.5 Than Pre-Omicron Infection Alone. Curr Issues Mol Biol 2023; 45:1741-1761. [PMID: 36826057 PMCID: PMC9955496 DOI: 10.3390/cimb45020112] [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: 01/31/2023] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Since the emergence of SARS-CoV-2 Omicron BA.1 and BA.2, several Omicron sublineages have emerged, supplanting their predecessors. Here we compared the neutralization of Omicron sublineages BA.1, BA.2, BA.4 and BA.5 by human sera collected from individuals who were infected with the ancestral B.1 (D614G) strain, who were vaccinated (3 doses) or with breakthrough infection with pre-Omicron strains (Gamma or Delta). All Omicron sublineages exhibited extensive escape from all sera when compared to the ancestral B.1 strain and to Delta, albeit to different levels depending on the origin of the sera. Convalescent sera were unable to neutralize BA.1, and partly neutralized BA.2, BA.4 and BA.5. Vaccinee sera partly neutralized BA.2, but BA.1, BA.4 and BA.5 evaded neutralizing antibodies (NAb). Some breakthrough infections (BTI) sera were non-neutralizing. Neutralizing BTI sera had similar neutralizing ability against all Omicron sublineages. Despite similar levels of anti-Spike and anti-Receptor Binding Domain (RBD) antibodies in all groups, BTI sera had the highest cross-neutralizing ability against all Omicron sublineages and convalescent sera were the least neutralizing. Antibody avidity inferred from the NT50:antibody titer ratio was highest in sera from BTI patients, underscoring qualitative differences in antibodies elicited by infection or vaccination. Together, these findings highlight the importance of vaccination to trigger highly cross-reactive antibodies that neutralize phylogenetically and antigenically distant strains, and suggest that immune imprinting by first generation vaccines may restrict, but not abolish, cross-neutralization.
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Affiliation(s)
- Eveline Santos da Silva
- HIV Clinical and Translational Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg
| | - Jean-Yves Servais
- HIV Clinical and Translational Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg
| | - Michel Kohnen
- Centre Hospitalier de Luxembourg, 4 Rue Ernest Barblé, L-1210 Luxembourg, Luxembourg
| | - Victor Arendt
- Centre Hospitalier de Luxembourg, 4 Rue Ernest Barblé, L-1210 Luxembourg, Luxembourg
| | - Georges Gilson
- Centre Hospitalier de Luxembourg, 4 Rue Ernest Barblé, L-1210 Luxembourg, Luxembourg
| | - Therese Staub
- Centre Hospitalier de Luxembourg, 4 Rue Ernest Barblé, L-1210 Luxembourg, Luxembourg
| | - Carole Seguin-Devaux
- HIV Clinical and Translational Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg
| | - Danielle Perez-Bercoff
- HIV Clinical and Translational Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg
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20
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Zhu Y, Saribas AS, Liu J, Lin Y, Bodnar B, Zhao R, Guo Q, Ting J, Wei Z, Ellis A, Li F, Wang X, Yang X, Wang H, Ho WZ, Yang L, Hu W. Protein expression/secretion boost by a novel unique 21-mer cis-regulatory motif (Exin21) via mRNA stabilization. Mol Ther 2023; 31:1136-1158. [PMID: 36793212 PMCID: PMC9927791 DOI: 10.1016/j.ymthe.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 10/24/2022] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Boosting protein production is invaluable in both industrial and academic applications. We discovered a novel expression-increasing 21-mer cis-regulatory motif (Exin21) that inserts between SARS-CoV-2 envelope (E) protein-encoding sequence and luciferase reporter gene. This unique Exin21 (CAACCGCGGTTCGCGGCCGCT), encoding a heptapeptide (QPRFAAA, designated as Qα), significantly (34-fold on average) boosted E production. Both synonymous and nonsynonymous mutations within Exin21 diminished its boosting capability, indicating the exclusive composition and order of 21 nucleotides. Further investigations demonstrated that Exin21/Qα addition could boost the production of multiple SARS-CoV-2 structural proteins (S, M, and N) and accessory proteins (NSP2, NSP16, and ORF3), and host cellular gene products such as IL-2, IFN-γ, ACE2, and NIBP. Exin21/Qα enhanced the packaging yield of S-containing pseudoviruses and standard lentivirus. Exin21/Qα addition on the heavy and light chains of human anti-SARS-CoV monoclonal antibody robustly increased antibody production. The extent of such boosting varied with protein types, cellular density/function, transfection efficiency, reporter dosage, secretion signaling, and 2A-mediated auto-cleaving efficiency. Mechanistically, Exin21/Qα increased mRNA synthesis/stability, and facilitated protein expression and secretion. These findings indicate that Exin21/Qα has the potential to be used as a universal booster for protein production, which is of importance for biomedicine research and development of bioproducts, drugs, and vaccines.
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Affiliation(s)
- Yuanjun Zhu
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - A. Sami Saribas
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Jinbiao Liu
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Yuan Lin
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Brittany Bodnar
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Ruotong Zhao
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Qian Guo
- Department of Medical Genetics & Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Julia Ting
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Zhengyu Wei
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Aidan Ellis
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Fang Li
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Xu Wang
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Xiaofeng Yang
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Hong Wang
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Wen-Zhe Ho
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Ling Yang
- Department of Medical Genetics & Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Wenhui Hu
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA; Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA.
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21
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Nanishi E, Borriello F, Seo HS, O’Meara TR, McGrath ME, Saito Y, Chen J, Diray-Arce J, Song K, Xu AZ, Barman S, Menon M, Dong D, Caradonna TM, Feldman J, Hauser BM, Schmidt AG, Baden LR, Ernst RK, Dillen C, Yu J, Chang A, Hilgers L, Platenburg PP, Dhe-Paganon S, Barouch DH, Ozonoff A, Zanoni I, Frieman MB, Dowling DJ, Levy O. Carbohydrate fatty acid monosulphate: oil-in-water adjuvant enhances SARS-CoV-2 RBD nanoparticle-induced immunogenicity and protection in mice. NPJ Vaccines 2023; 8:18. [PMID: 36788219 PMCID: PMC9927065 DOI: 10.1038/s41541-023-00610-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/24/2023] [Indexed: 02/16/2023] Open
Abstract
Development of SARS-CoV-2 vaccines that protect vulnerable populations is a public health priority. Here, we took a systematic and iterative approach by testing several adjuvants and SARS-CoV-2 antigens to identify a combination that elicits antibodies and protection in young and aged mice. While demonstrating superior immunogenicity to soluble receptor-binding domain (RBD), RBD displayed as a protein nanoparticle (RBD-NP) generated limited antibody responses. Comparison of multiple adjuvants including AddaVax, AddaS03, and AS01B in young and aged mice demonstrated that an oil-in-water emulsion containing carbohydrate fatty acid monosulphate derivative (CMS:O/W) most effectively enhanced RBD-NP-induced cross-neutralizing antibodies and protection across age groups. CMS:O/W enhanced antigen retention in the draining lymph node, induced injection site, and lymph node cytokines, with CMS inducing MyD88-dependent Th1 cytokine polarization. Furthermore, CMS and O/W synergistically induced chemokine production from human PBMCs. Overall, CMS:O/W adjuvant may enhance immunogenicity and protection of vulnerable populations against SARS-CoV-2 and other infectious pathogens.
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Affiliation(s)
- Etsuro Nanishi
- grid.2515.30000 0004 0378 8438Precision Vaccines Program, Boston Children’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Pediatrics, Harvard Medical School, Boston, MA USA
| | - Francesco Borriello
- grid.2515.30000 0004 0378 8438Precision Vaccines Program, Boston Children’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Pediatrics, Harvard Medical School, Boston, MA USA ,grid.2515.30000 0004 0378 8438Division of Immunology, Boston Children’s Hospital, Boston, MA USA ,Present Address: Generate Biomedicines, Cambridge, MA USA
| | - Hyuk-Soo Seo
- grid.65499.370000 0001 2106 9910Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA USA
| | - Timothy R. O’Meara
- grid.2515.30000 0004 0378 8438Precision Vaccines Program, Boston Children’s Hospital, Boston, MA USA
| | - Marisa E. McGrath
- grid.411024.20000 0001 2175 4264Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD USA
| | - Yoshine Saito
- grid.2515.30000 0004 0378 8438Precision Vaccines Program, Boston Children’s Hospital, Boston, MA USA
| | - Jing Chen
- grid.2515.30000 0004 0378 8438Research Computing Group, Boston Children’s Hospital, Boston, MA USA
| | - Joann Diray-Arce
- grid.2515.30000 0004 0378 8438Precision Vaccines Program, Boston Children’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Pediatrics, Harvard Medical School, Boston, MA USA
| | - Kijun Song
- grid.65499.370000 0001 2106 9910Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Andrew Z. Xu
- grid.65499.370000 0001 2106 9910Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Soumik Barman
- grid.2515.30000 0004 0378 8438Precision Vaccines Program, Boston Children’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Pediatrics, Harvard Medical School, Boston, MA USA
| | - Manisha Menon
- grid.2515.30000 0004 0378 8438Precision Vaccines Program, Boston Children’s Hospital, Boston, MA USA
| | - Danica Dong
- grid.2515.30000 0004 0378 8438Precision Vaccines Program, Boston Children’s Hospital, Boston, MA USA
| | - Timothy M. Caradonna
- grid.461656.60000 0004 0489 3491Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA USA
| | - Jared Feldman
- grid.461656.60000 0004 0489 3491Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA USA
| | - Blake M. Hauser
- grid.461656.60000 0004 0489 3491Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA USA
| | - Aaron G. Schmidt
- grid.461656.60000 0004 0489 3491Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA USA ,grid.38142.3c000000041936754XDepartment of Microbiology, Harvard Medical School, Boston, MA USA
| | - Lindsey R. Baden
- grid.62560.370000 0004 0378 8294Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA
| | - Robert K. Ernst
- grid.411024.20000 0001 2175 4264Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD USA
| | - Carly Dillen
- grid.411024.20000 0001 2175 4264Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD USA
| | - Jingyou Yu
- grid.38142.3c000000041936754XCenter for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA USA
| | - Aiquan Chang
- grid.38142.3c000000041936754XCenter for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA USA
| | | | | | - Sirano Dhe-Paganon
- grid.65499.370000 0001 2106 9910Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA USA
| | - Dan H. Barouch
- grid.38142.3c000000041936754XCenter for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA USA
| | - Al Ozonoff
- grid.2515.30000 0004 0378 8438Precision Vaccines Program, Boston Children’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Pediatrics, Harvard Medical School, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT & Harvard, Cambridge, MA USA
| | - Ivan Zanoni
- grid.38142.3c000000041936754XDepartment of Pediatrics, Harvard Medical School, Boston, MA USA ,grid.2515.30000 0004 0378 8438Division of Immunology, Boston Children’s Hospital, Boston, MA USA
| | - Matthew B. Frieman
- grid.411024.20000 0001 2175 4264Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD USA
| | - David J. Dowling
- grid.2515.30000 0004 0378 8438Precision Vaccines Program, Boston Children’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Pediatrics, Harvard Medical School, Boston, MA USA
| | - Ofer Levy
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT & Harvard, Cambridge, MA, USA.
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22
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Wang Q, Ye S, Zhou Z, Song A, Zhu X, Peng J, Liang R, Yang C, Yu X, Huang X, Yu J, Qiu Y, Ge X. Key mutations in the spike protein of SARS-CoV-2 affecting neutralization resistance and viral internalization. J Med Virol 2023; 95:e28407. [PMID: 36519597 PMCID: PMC9877909 DOI: 10.1002/jmv.28407] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/17/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
To control the ongoing COVID-19 pandemic, a variety of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines have been developed. However, the rapid mutations of SARS-CoV-2 spike (S) protein may reduce the protective efficacy of the existing vaccines which is mainly determined by the level of neutralizing antibodies targeting S. In this study, we screened prevalent S mutations and constructed 124 pseudotyped lentiviral particles carrying these mutants. We challenged these pseudoviruses with sera vaccinated by Sinovac CoronaVac and ZF2001 vaccines, two popular vaccines designed for the initial strain of SARS-CoV-2, and then systematically assessed the susceptivity of these SARS-CoV-2 variants to the immune sera of vaccines. As a result, 14 S mutants (H146Y, V320I + S477N, V382L, K444R, L455F + S477N, L452M + F486L, F486L, Y508H, P521R, A626S, S477N + S698L, A701V, S477N + T778I, E1144Q) were found to be significantly resistant to neutralization, indicating reduced protective efficacy of the vaccines against these SARS-CoV-2 variants. In addition, F486L and Y508H significantly enhanced the utilization of human angiotensin-converting enzyme 2, suggesting a potentially elevated infectivity of these two mutants. In conclusion, our results show that some prevalent S mutations of SARS-CoV-2 reduced the protective efficacy of current vaccines and enhance the infectivity of the virus, indicating the necessity of vaccine renewal and providing direction for the development of new vaccines.
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Affiliation(s)
- Qiong Wang
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Sheng‐Bao Ye
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Zhi‐Jian Zhou
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - A‐Ling Song
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Xi Zhu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Jia‐Mei Peng
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Rui‐Min Liang
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Chen‐Hui Yang
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Xiao‐Wei Yu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina,Hunan Prevention and Treatment Institute for Occupational DiseasesChangshaHunanChina
| | - Xun Huang
- Department of Hospital Infection Control CenterXiangya Hospital of Central South UniversityChangshaChina
| | - Jie Yu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Ye Qiu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Xing‐Yi Ge
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina,Department of Hospital Infection Control CenterXiangya Hospital of Central South UniversityChangshaChina
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23
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SARS-CoV-2 neutralizing antibody response in vaccinated and non-vaccinated hospital healthcare workers with or without history of infection. Microbes Infect 2023; 25:105077. [PMID: 36400331 PMCID: PMC9664837 DOI: 10.1016/j.micinf.2022.105077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/06/2022] [Indexed: 11/17/2022]
Abstract
Between March 2021 and February 2022, SARS-CoV-2 neutralizing antibodies dynamics was investigated in a prospective observational study in 903 healthcare workers of a hospital in Switzerland. A surrogate neutralization assay measuring the competitive inhibition of the angiotensin converting enzyme 2 (ACE2) binding to the spike protein (S) of the SARS-CoV-2 wild type virus and to five variants of concern (Alpha, Beta, Gamma, Delta, Omicron) was used. We observed a broad distribution of neutralization activity among participants and substantial differences in neutralizing titers against variants. Participants were grouped based on combinations of vaccination status (1, 2 or 3 doses) and/or prior or subsequent SARS-CoV-2 infection/reinfection. Triple vaccination resulted in the highest neutralization response, as did double vaccination with prior or subsequent infection. Double vaccination without infection showed an intermediate neutralization response while SARS-CoV-2 infection in non-vaccinated participants resulted in poor neutralization response. After triple vaccination or double vaccination plus infection, additional vaccination and/or reinfection had no impact on neutralizing antibody titers over the observed period. These results strongly support the booster dose strategy, while additional booster doses within short time intervals might not improve immunization. However, dynamics of neutralizing antibodies titers needs to be monitored individually, over time and include newly emerging variants.
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24
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Yakoubi A, Dhafer CEB. Advanced Plasmonic Nanoparticle-Based Techniques for the Prevention, Detection, and Treatment of Current COVID-19. PLASMONICS (NORWELL, MASS.) 2022; 18:311-347. [PMID: 36588744 PMCID: PMC9786532 DOI: 10.1007/s11468-022-01754-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/20/2022] [Indexed: 06/16/2023]
Abstract
Coronavirus is an ongoing global pandemic caused by severe acute respiratory syndrome coronavirus 2. Coronavirus disease 2019 known as COVID-19 is the worst pandemic since World War II. The outbreak of COVID-19 had a significant repercussion on the health, economy, politics, and environment, making coronavirus-related issues more complicated and becoming one of the most challenging pandemics of the last century with deadly outcomes and a high rate of the reproduction number. There are thousands of different types - or variants - of COVID circulating across the world. Viruses mutate all the time; it emphasizes the critical need for the designing of efficient vaccines to prevent virus infection, early and fast diagnosis, and effective antiviral and protective therapeutics. In this regard, the use of nanotechnology offers new opportunities for the development of novel strategies in terms of prevention, diagnosis, and treatment of COVID-19. This review presents an outline of the platforms developed using plasmonic nanoparticles in the detection, treatment, and prevention of SARS-CoV-2. We select the best strategies in each of these approaches. The properties of metallic plasmon NPs and their relevance in the development of novel point-of-care diagnosis approaches for COVID-19 are highlighted. Also, we discuss the current challenges and the future perspectives looking towards the clinical translation and the commercial aspects of nanotechnology and plasmonic NP-based diagnostic tools and therapy to fight COVID-19 pandemic. The article could be of significance for researchers dedicated to developing suitable plasmonic detection tools and therapy approaches for COVID-19 viruses and future pandemics.
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Affiliation(s)
- Afef Yakoubi
- Laboratory of Hetero-organic Compounds and Nanostructured Materials, Chemistry Department, Faculty of Sciences Bizerte, University of Carthage, LR 18 ES11, 7021 Bizerte, Tunisia
| | - Cyrine El Baher Dhafer
- Chemistry Department College of Science, Jouf University, P.O Box: 2014, Sakaka, Saudi Arabia
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25
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Kwon HJ, Kosikova M, Tang W, Ortega-Rodriguez U, Radvak P, Xiang R, Mercer KE, Muskhelishvili L, Davis K, Ward JM, Kosik I, Holly J, Kang I, Yewdell JW, Plant EP, Chen WH, Shriver MC, Barnes RS, Pasetti MF, Zhou B, Wentworth DE, Xie H. Enhanced virulence and waning vaccine-elicited antibodies account for breakthrough infections caused by SARS-CoV-2 delta and beyond. iScience 2022; 25:105507. [PMID: 36373096 PMCID: PMC9635945 DOI: 10.1016/j.isci.2022.105507] [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: 08/14/2022] [Revised: 10/05/2022] [Accepted: 11/01/2022] [Indexed: 11/08/2022] Open
Abstract
Here we interrogate the factors responsible for SARS-CoV-2 breakthrough infections in a K18-hACE2 transgenic mouse model. We show that Delta and the closely related Kappa variant cause viral pneumonia and severe lung lesions in K18-hACE2 mice. Human COVID-19 mRNA post-vaccination sera after the 2nd dose are significantly less efficient in neutralizing Delta/Kappa than early 614G virus in vitro and in vivo. By 5 months post-vaccination, ≥50% of donors lack detectable neutralizing antibodies against Delta and Kappa and all mice receiving 5-month post-vaccination sera die after the lethal challenges. Although a 3rd vaccine dose can boost antibody neutralization against Delta in vitro and in vivo, the mean log neutralization titers against the latest Omicron subvariants are 1/3-1/2 of those against the original 614D virus. Our results suggest that enhanced virulence, greater immune evasion, and waning of vaccine-elicited protection account for SARS-CoV-2 variants caused breakthrough infections.
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Affiliation(s)
- Hyung-Joon Kwon
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Martina Kosikova
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Weichun Tang
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Uriel Ortega-Rodriguez
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Peter Radvak
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Ruoxuan Xiang
- Division of Biostatistics, Office of Biostatistics and Epidemiology, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Kelly E. Mercer
- Biomarkers and Alternative Models Branch, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, AR, USA
| | | | - Kelly Davis
- Toxicologic Pathology Associates, Jefferson, AR, USA
| | | | - Ivan Kosik
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jaroslav Holly
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Insung Kang
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Jonathan W. Yewdell
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ewan P. Plant
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Wilbur H. Chen
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mallory C. Shriver
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Robin S. Barnes
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Marcela F. Pasetti
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Bin Zhou
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - David E. Wentworth
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Hang Xie
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
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26
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Serum Fc-Mediated Monocyte Phagocytosis Activity Is Stable for Several Months after SARS-CoV-2 Asymptomatic and Mildly Symptomatic Infection. Microbiol Spectr 2022; 10:e0183722. [PMID: 36374040 PMCID: PMC9769986 DOI: 10.1128/spectrum.01837-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We investigated the temporal profile of multiple components of the serological response after asymptomatic or mildly symptomatic SARS-CoV-2 infection, in a cohort of 67 previously SARS-CoV-2 naive young adults, up to 8.5 months after infection. We found a significant decrease of spike IgG and neutralization antibody titers from early (11 to 56 days) to late (4 to 8.5 months) time points postinfection. Over the study period, S1-specific IgG levels declined significantly faster than that of the S2-specific IgG. Further, serum antibodies from PCR-confirmed participants cross-recognized S2, but not S1, of the betacoronaviruses HKU1 and OC43, suggesting a greater degree of cross-reactivity of S2 among betacoronaviruses. Antibody-Dependent Natural Killer cell Activation (ADNKA) was detected at the early time point but significantly decreased at the late time point. Induction of serum Antibody-Dependent Monocyte Phagocytosis (ADMP) was detected in all the infected participants, and its levels remained stable over time. Additionally, a reduced percentage of participants had detectable neutralizing activity against the Beta (50%), Gamma (61 to 67%), and Delta (90 to 94%) variants, both early and late postinfection, compared to the ancestral strain (100%). Antibody binding to S1 and RBD of Beta, Gamma, Delta (1.7 to 2.3-fold decrease), and Omicron (10 to 16-fold decrease) variants was also significantly reduced compared to the ancestral SARS-CoV-2 strain. Overall, we found variable temporal profiles of specific components and functionality of the serological response to SARS-CoV-2 in young adults, which is characterized by lasting, but decreased, neutralizing activity and antibody binding to S1, stable ADMP activity, and relatively stable S2-specific IgG levels. IMPORTANCE Adaptive immunity mediated by antibodies is important for controlling SARS-CoV-2 infection. While vaccines against COVID-19 are currently widely distributed, a high proportion of the global population is still unvaccinated. Therefore, understanding the dynamics and maintenance of the naive humoral immune response to SARS-CoV-2 is of great importance. In addition, long-term responses after asymptomatic infection are not well-characterized, given the challenges in identifying such cases. Here, we investigated the longitudinal humoral profile in a well-characterized cohort of young adults with documented asymptomatic or mildly symptomatic SARS-CoV-2 infection. By analyzing samples collected preinfection, early after infection and during late convalescence, we found that, while neutralizing activity decreased over time, high levels of serum S2 IgG and Antibody-Dependent Monocyte Phagocytosis (ADMP) activity were maintained up to 8.5 months after infection. This suggests that a subset of antibodies with specific functions could contribute to long-term protection against SARS-CoV-2 in convalescent unvaccinated individuals.
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Abavisani M, Rahimian K, Mahdavi B, Tokhanbigli S, Mollapour Siasakht M, Farhadi A, Kodori M, Mahmanzar M, Meshkat Z. Mutations in SARS-CoV-2 structural proteins: a global analysis. Virol J 2022; 19:220. [PMID: 36528612 PMCID: PMC9759450 DOI: 10.1186/s12985-022-01951-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Emergence of new variants mainly variants of concerns (VOC) is caused by mutations in main structural proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Therefore, we aimed to investigate the mutations among structural proteins of SARS-CoV-2 globally. METHODS We analyzed samples of amino-acid sequences (AASs) for envelope (E), membrane (M), nucleocapsid (N), and spike (S) proteins from the declaration of the coronavirus 2019 (COVID-19) as pandemic to January 2022. The presence and location of mutations were then investigated by aligning the sequences to the reference sequence and categorizing them based on frequency and continent. Finally, the related human genes with the viral structural genes were discovered, and their interactions were reported. RESULTS The results indicated that the most relative mutations among the E, M, N, and S AASs occurred in the regions of 7 to 14, 66 to 88, 164 to 205, and 508 to 635 AAs, respectively. The most frequent mutations in E, M, N, and S proteins were T9I, I82T, R203M/R203K, and D614G. D614G was the most frequent mutation in all six geographical areas. Following D614G, L18F, A222V, E484K, and N501Y, respectively, were ranked as the most frequent mutations in S protein globally. Besides, A-kinase Anchoring Protein 8 Like (AKAP8L) was shown as the linkage unit between M, E, and E cluster genes. CONCLUSION Screening the structural protein mutations can help scientists introduce better drug and vaccine development strategies.
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Affiliation(s)
- Mohammad Abavisani
- grid.411583.a0000 0001 2198 6209Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran ,grid.411583.a0000 0001 2198 6209Department of Microbiology and Virology, School of Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Karim Rahimian
- grid.46072.370000 0004 0612 7950Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Bahar Mahdavi
- grid.417689.5Department of Molecular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Samaneh Tokhanbigli
- grid.411463.50000 0001 0706 2472Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences and Technology, Pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Mahsa Mollapour Siasakht
- grid.5645.2000000040459992XDepartment of Biochemistry, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Amin Farhadi
- grid.412462.70000 0000 8810 3346Department of Biology, Payame Noor University, Tehran, Iran
| | - Mansoor Kodori
- grid.510756.00000 0004 4649 5379Non Communicable Diseases Research Center, Bam University of Medical Sciences, Bam, Iran
| | - Mohammadamin Mahmanzar
- grid.46072.370000 0004 0612 7950Department of Bioinformatics, Kish International Campus University of Tehran, Kish, Iran
| | - Zahra Meshkat
- grid.411583.a0000 0001 2198 6209Department of Microbiology and Virology, School of Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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28
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Yu TC, Thornton ZT, Hannon WW, DeWitt WS, Radford CE, Matsen FA, Bloom JD. A biophysical model of viral escape from polyclonal antibodies. Virus Evol 2022; 8:veac110. [PMID: 36582502 PMCID: PMC9793855 DOI: 10.1093/ve/veac110] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/12/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
A challenge in studying viral immune escape is determining how mutations combine to escape polyclonal antibodies, which can potentially target multiple distinct viral epitopes. Here we introduce a biophysical model of this process that partitions the total polyclonal antibody activity by epitope and then quantifies how each viral mutation affects the antibody activity against each epitope. We develop software that can use deep mutational scanning data to infer these properties for polyclonal antibody mixtures. We validate this software using a computationally simulated deep mutational scanning experiment and demonstrate that it enables the prediction of escape by arbitrary combinations of mutations. The software described in this paper is available at https://jbloomlab.github.io/polyclonal.
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Affiliation(s)
- Timothy C Yu
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Computational Biology Program, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, 1959 NE Pacifc Street, Seattle, WA 98195, USA
| | - Zorian T Thornton
- Computational Biology Program, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
| | - William W Hannon
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Computational Biology Program, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, 1959 NE Pacifc Street, Seattle, WA 98195, USA
| | - William S DeWitt
- Computational Biology Program, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
| | - Caelan E Radford
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Computational Biology Program, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, 1959 NE Pacifc Street, Seattle, WA 98195, USA
| | - Frederick A Matsen
- Computational Biology Program, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Computational Biology Program, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, 1100 Fairview Ave N, Seattle, WA 98109, USA
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29
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Gul I, Kamal MA. Experimental and Computational Approaches for SARS-CoV-2 Theranostics. Curr Pharm Des 2022; 28:i-ii. [PMID: 36650977 DOI: 10.2174/138161282846221227231152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Ijaz Gul
- Shenzhen International Graduate School, Tsinghua University, China
| | - Mohammad Amjad Kamal
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, China.,King Fahd Medical Research Center, King Abdulaziz University, Saudi Arabia.,Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Bangladesh.,Enzymoics, 7 Peterlee place, Hebersham, NSW 2770; Novel Global Community Educational Foundation, Australia
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30
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Li XF, Zhang NN, Li YH, Cao SC, Zhang YF, Qin CF. Neutralization of ARCoV-induced sera against SARS-CoV-2 variants. Hum Vaccin Immunother 2022; 18:2094142. [PMID: 35816411 DOI: 10.1080/21645515.2022.2094142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
ARCoV is a candidate mRNA vaccine encoding receptor-binding domain of SARS-CoV-2. Its safety, tolerability, and immunogenicity profile have been confirmed in the phase 1 clinical trial in China. A multi-regional phase 3 clinical trial is currently underway to test the efficacy of ARCoV (NCT04847102). Here, we tested the cross-neutralization against SARS-CoV-2 variants of concern (VOCs) of a panel of serum samples from participants in the phase 1 clinical trial of ARCoV by pesudo- and authentic SARS-CoV-2. Our data suggest the immunity induced by the ARCoV vaccine reduced but still has significant neutralization against the Alpha and Delta variants. Moreover, ARCoV maintained activity against the Beta variant, despite of its obvious reduction in neutralizing titers. Our findings further support the solid protective neutralization activity against VOCs induced by ARCoV vaccine.
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Affiliation(s)
- Xiao-Feng Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Na-Na Zhang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.,School of Medicine, Tsinghua University, Beijing, China
| | - Yu-Hua Li
- Department of Arbovirus Vaccine, National Institutes for Food and Drug Control, Beijing, China
| | - Shou-Chun Cao
- Department of Arbovirus Vaccine, National Institutes for Food and Drug Control, Beijing, China
| | - Yi-Fei Zhang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Cheng-Feng Qin
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.,School of Medicine, Tsinghua University, Beijing, China
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31
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Higashimoto Y, Kozawa K, Miura H, Kawamura Y, Ihira M, Hiramatsu H, Suzuki R, Haga K, Takai-Todaka R, Sawada A, Katayama K, Yoshikawa T. Correlation between anti-S IgG and neutralizing antibody titers against three live SARS-CoV-2 variants in BNT162b2 vaccine recipients. Hum Vaccin Immunother 2022; 18:2105611. [PMID: 36094467 DOI: 10.1080/21645515.2022.2105611] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We analyzed serially collected serum samples from healthy adults who underwent BNT162b2 vaccination to elucidate the association between spike (S)-IgG antibody titers determined by ELISA using the WHO international standard (NIBSC code 20/136) and neutralizing antibody titers against three live SARS-CoV-2 variants. This study included 53 health care workers who received two doses of the BNT162b2 vaccine. S-IgG and nucleocapsid (N)-IgG antibody titers were measured by ELISA. Neutralizing (NT) antibody responses against three variants (Wuhan D614 G: KUH003, Alpha, and Delta) were evaluated before and after the first and second vaccination. N-IgG were not detected in any serum samples. S-IgG antibody titers remarkably increased after two BNT162b2 vaccine doses in all participants. S-IgG antibody titers were strongly correlated with NT titers against three variants of live viruses: KUH003 (r = 0.86), Alpha (r = 0.72), and Delta (r = 0.84). Serum samples from participants after one dose of BNT162b2 neutralized Alpha efficiently (median titer, 113.0), but median NT titers against KUH003 and Delta variants were lower, 57.0 and 28.0, respectively (p < .01). Two doses of the BNT162b2 vaccine elicited a strong immune response in this study. The second dose was required for induction of a strong booster effect. Serum collected from BNT162b2 vaccine recipients contained significantly lower neutralizing activity against Delta than that of against KUH003 (p < .0001) and Alpha (p < .0001). If a new variant emerges, live virus-based NT titers should be examined in serum obtained from vaccine recipients to evaluate vaccine efficacy for protection against infection.
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Affiliation(s)
- Yuki Higashimoto
- Faculty of Medical Technology, Fujita Health University School of Medical Sciences, Toyoake, Aichi, Japan
| | - Kei Kozawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Hiroki Miura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Yoshiki Kawamura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Masaru Ihira
- Faculty of Clinical Engineering, Fujita Health University School of Medical Sciences, Toyoake, Aichi, Japan
| | - Hiroyuki Hiramatsu
- Department of Clinical Pharmacy, Fujita Health University Hospital, Toyoake, Aichi, Japan
| | - Ryota Suzuki
- Department of Clinical Pharmacy, Fujita Health University Hospital, Toyoake, Aichi, Japan
| | - Kei Haga
- Laboratory of Viral Infection Control, Department of Infection Control Science and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Reiko Takai-Todaka
- Laboratory of Viral Infection Control, Department of Infection Control Science and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Akihito Sawada
- Laboratory of Viral Infection Control, Department of Infection Control Science and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection Control, Department of Infection Control Science and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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32
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Pons S, Uhel F, Frapy E, Sérémé Y, Zafrani L, Aschard H, Skurnik D. How Protective are Antibodies to SARS-CoV-2, the Main Weapon of the B-Cell Response? Stem Cell Rev Rep 2022; 19:585-600. [PMID: 36422774 PMCID: PMC9685122 DOI: 10.1007/s12015-022-10477-y] [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] [Accepted: 11/03/2022] [Indexed: 11/25/2022]
Abstract
Since the beginning of the Coronavirus disease (COVID)-19 pandemic in December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been responsible for more than 600 million infections and 6.5 million deaths worldwide. Given the persistence of SARS-CoV-2 and its ability to develop new variants, the implementation of an effective and long-term herd immunity appears to be crucial to overcome the pandemic. While a vast field of research has focused on the role of humoral immunity against SARS-CoV-2, a growing body of evidence suggest that antibodies alone only confer a partial protection against infection of reinfection which could be of high importance regarding the strategic development goals (SDG) of the United Nations (UN) and in particular UN SDG3 that aims towards the realization of good health and well being on a global scale in the context of the COVID-19 pandemic.In this review, we highlight the role of humoral immunity in the host defense against SARS-CoV-2, with a focus on highly neutralizing antibodies. We summarize the results of the main clinical trials leading to an overall disappointing efficacy of convalescent plasma therapy, variable results of monoclonal neutralizing antibodies in patients with COVID-19 but outstanding results for the mRNA based vaccines against SARS-CoV-2. Finally, we advocate that beyond antibody responses, the development of a robust cellular immunity against SARS-CoV-2 after infection or vaccination is of utmost importance for promoting immune memory and limiting disease severity, especially in case of (re)-infection by variant viruses.
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Affiliation(s)
- Stéphanie Pons
- DMU DREAM, Department of Anesthesiology and Critical Care, Sorbonne University, GRC 29, AP-HP, Pitié-Salpêtrière, Paris, France
- Université de Paris Cité, INSERM U976- Human Immunology, Pathophysiology, Immunotherapy (HIPI), Paris, France
| | - Fabrice Uhel
- INSERM, CNRS, Institut Necker Enfants Malades, Université de Paris Cité, Paris, France
- DMU ESPRIT, Médecine Intensive Réanimation, AP-HP, Hôpital Louis Mourier, 92700, Colombes, France
| | - Eric Frapy
- INSERM, CNRS, Institut Necker Enfants Malades, Université de Paris Cité, Paris, France
| | - Youssouf Sérémé
- INSERM, CNRS, Institut Necker Enfants Malades, Université de Paris Cité, Paris, France
| | - Lara Zafrani
- Université de Paris Cité, INSERM U976- Human Immunology, Pathophysiology, Immunotherapy (HIPI), Paris, France
- Medical Intensive Care Unit, Saint Louis Hospital, Assistance Publique Hôpitaux de Paris (APHP), Université de Paris, Paris, France
| | - Hugues Aschard
- Department of Computational Biology, USR 3756 CNRS, Institut Pasteur, Paris, France
| | - David Skurnik
- INSERM, CNRS, Institut Necker Enfants Malades, Université de Paris Cité, Paris, France.
- Department of Clinical Microbiology, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Université de Paris Cité, Paris, France.
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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33
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Rosen B, Davidovitch N, Chodick G, Israeli A. The role of Israeli researchers in the scientific literature regarding COVID-19 vaccines. Isr J Health Policy Res 2022; 11:39. [PMID: 36419188 PMCID: PMC9684862 DOI: 10.1186/s13584-022-00548-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/03/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The accurate and timely publication of scientific findings is a key component of the global response to the COVID-19 pandemic. This article explores the role of Israeli researchers in the scientific literature regarding COVID-19 vaccines. METHODS Content and bibliometric analysis of articles included in the Web of Science database regarding COVID-19 vaccines, that were published between January 2020 and June 2022. RESULTS The Web of Science includes 18,596 articles regarding COVID-19 vaccines that were published between January 2020 and June 2022. 536 (3%) of those articles had at least one Israeli author. These "Israeli articles" accounted for 11% of the NEJM articles on COVID-19 vaccines, 9% of such articles in Nature Medicine, and 4% of such articles in the Lancet. 80 of the 536 Israeli articles (15%) were recognized as "Highly Cited Papers" (articles that rank in the top 1% by citations for field and publication year). Most of the Israeli Highly Cited Papers (HCPs) analyzed the safety and/or efficacy of the COVID-19 vaccine developed by Pfizer and BioNTech (BNT162b2). Most of the Israeli HCPs made use of detailed and comprehensive individual data available from Israel's health plans, hospitals, or Ministry of Health. The 15% HCP rate (i.e., the number of HCPs divided by the number of all articles) for the Israeli articles was triple the HCP rate for all articles on COVID-19 vaccines (5%). A key factor contributing to Israel's prominent role in rapid publication of vaccination impact studies was Israel's being a world leader in the initial vaccination rollout, the administration of boosters, and the vaccination of pregnant women. Other contributing factors include Israeli researchers' access to well-developed electronic health record systems linking vaccinations and outcomes, the analytic strengths of leading Israeli researchers and research institutions, collaborations with leading research institutions in other countries, and the ability to quickly identify emerging research opportunities and mobilize accordingly. Recent developments in the priorities and selection criteria of leading journals have also played a role; these include an increased openness to well-designed observational studies and to manuscripts from outside of Europe and North America. CONCLUSIONS Israeli researchers, Israeli research institutions, and the Israeli government can, and should, take concrete steps to build upon lessons learned in the course of the recent surge of high-quality publications related to COVID-19 vaccines (such as the value of linking data across organizations). These lessons can be applied to a wide range of fields, including fields that go well beyond vaccines and pandemic responses.
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Affiliation(s)
- Bruce Rosen
- grid.419640.e0000 0001 0845 7919Myers-JDC-Brookdale Institute, Jerusalem, Israel ,grid.9619.70000 0004 1937 0538Paul Baerwald School of Social Work and Social Welfare, Hebrew University, Jerusalem, Israel
| | - Nadav Davidovitch
- grid.7489.20000 0004 1937 0511School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beersheva, Israel ,Taub Center for Social Policy Studies in Israel, Jerusalem, Israel
| | - Gabriel Chodick
- grid.425380.8Maccabi Healthcare Services, Tel Aviv, Israel ,grid.12136.370000 0004 1937 0546Tel Aviv University, Tel Aviv, Israel
| | - Avi Israeli
- grid.9619.70000 0004 1937 0538Hebrew University Hadassah Medical School, Jerusalem, Israel ,grid.414840.d0000 0004 1937 052XMinistry of Health, Jerusalem, Israel
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Jeong BS, Jeon JY, Lai CJ, Yun HY, Jung JU, Oh BH. Structural basis for the broad and potent cross-reactivity of an N501Y-centric antibody against sarbecoviruses. Front Immunol 2022; 13:1049867. [PMID: 36466915 PMCID: PMC9714666 DOI: 10.3389/fimmu.2022.1049867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/24/2022] [Indexed: 11/18/2022] Open
Abstract
More than 80% of SARS-CoV-2 variants, including Alpha and Omicron, contain an N501Y mutation in the receptor-binding domain (RBD) of the spike protein. The N501Y change is an adaptive mutation enabling tighter interaction with the human ACE2 receptor. We have developed a broadly neutralizing antibody (nAb), D27LEY, whose binding affinity was intentionally optimized for Y501. This N501Y-centric antibody not only interacts with the Y501-containing RBDs of SARS-CoV-2 variants, including Omicron, with pico- or subnanomolar binding affinity, but also binds tightly to the RBDs with a different amino acid at residue 501. The crystal structure of the Fab fragment of D27LEY bound to the RBD of the Alpha variant reveals that the Y501-containing loop adopts a ribbon-like topology and serves as a small but major epitope in which Y501 is a part of extensive intermolecular interactions. A hydrophobic cleft on the most conserved surface of the RBD core serves as another major binding epitope. These data explain the broad and potent cross-reactivity of this N501Y-centric antibody, and suggest that a vaccine antigenic component composed of the RBD core and a part of receptor-binding motif (RBM) containing tyrosine at residue 501 might elicit broad and potent humoral responses across sarbecoviruses.
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Affiliation(s)
- Bo-Seong Jeong
- Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Joon Young Jeon
- Department of Protein Design, Therazyne, lnc., Daejeon, South Korea
| | - Chih-Jen Lai
- Cancer Biology Department, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | | | - Jae U. Jung
- Cancer Biology Department, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Byung-Ha Oh
- Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- Department of Protein Design, Therazyne, lnc., Daejeon, South Korea
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Zhu Y, Hu Y, Liu N, Chong H, He Y. Potent inhibition of diverse Omicron sublineages by SARS-CoV-2 fusion-inhibitory lipopeptides. Antiviral Res 2022; 208:105445. [PMID: 36265805 PMCID: PMC9574594 DOI: 10.1016/j.antiviral.2022.105445] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/03/2022] [Accepted: 10/10/2022] [Indexed: 11/05/2022]
Abstract
The emergence and rapid spreading of SARS-CoV-2 variants of concern (VOCs) have posed a great challenge to the efficacy of vaccines and therapeutic antibodies, calling for antivirals that can overcome viral evasion. We recently reported that SARS-CoV-2 fusion-inhibitory lipopeptides, IPB02V3 and IPB24, possessed the potent activities against divergent VOCs, including Alpha, Beta, Gamma, Delta, and the initial Omicron strain (B.1.1.529); however, multiple Omicron sublineages have emerged and BA.4/5 is now becoming predominant globally. In this study, we focused on characterizing the functionality of the spike (S) proteins derived from Omicron sublineages and their susceptibility to the inhibition of IPB02V3 and IPB24. We first found that the S proteins of BA.2, BA.2.12.1, BA.3, and BA.4/5 exhibited significantly increased cell fusion capacities compared to BA.1, whereas the pseudoviruses of BA.2.12.1, BA.3, and BA.4/5 had significantly increased infectivity relative to BA.1 or BA.2. Next, we verified that IPB02V3 and IPB24 also maintained their very high potent activities in inhibiting diverse Omicron sublineages, even with enhanced potencies relative to the inhibition on ancestral virus. Moreover, we demonstrated that evolved Omicron mutations in the inhibitor-binding heptad repeat 1 (HR1) site could impair the S protein-driven cell fusogenicity and infectivity, but none of single or combined mutations affected the antiviral activity of IPB02V3 and IPB24. Therefore, we believe that viral fusion inhibitors possess high potential to be developed as effective drugs for fighting SARS-CoV-2 variants including diverse Omicron sublineages.
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Affiliation(s)
- Yuanmei Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Yue Hu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Nian Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Huihui Chong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Yuxian He
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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Wu T, Zhu Y, Liu N, Hu Y, Chong H, He Y. Resistance profile and mechanism of severe acute respiratory syndrome coronavirus-2 variants to LCB1 inhibitor targeting the spike receptor-binding motif. Front Microbiol 2022; 13:1022006. [PMID: 36304946 PMCID: PMC9593036 DOI: 10.3389/fmicb.2022.1022006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
LCB1 is a 56-mer miniprotein computationally designed to target the spike (S) receptor-binding motif of SARS-CoV-2 with potent in vitro and in vivo inhibitory activities (Cao et al., 2020; Case et al., 2021). However, the rapid emergence and epidemic of viral variants have greatly impacted the effectiveness of S protein-targeting vaccines and antivirals. In this study, we chemically synthesized a peptide-based LCB1 inhibitor and characterized the resistance profile and underlying mechanism of SARS-CoV-2 variants. Among five variants of concern (VOCs), we found that pseudoviruses of Beta, Gamma, and Omicron were highly resistant to the LCB1 inhibition, whereas the pseudoviruses of Alpha and Delta as well as the variant of interest (VOI) Lambda only caused mild resistance. By generating a group of mutant viruses carrying single or combination mutations, we verified that K417N and N501Y substitutions in RBD critically determined the high resistance phenotype of VOCs. Furthermore, a large panel of 85 pseudoviruses with naturally occurring RBD point-mutations were generated and applied to LCB1, which identified that E406Q, K417N, and L455F conferred high-levels of resistance, when Y505W caused a ∼6-fold resistance fold-change. We also showed that the resistance mutations could greatly weaken the binding affinity of LCB1 to RBD and thus attenuated its blocking capacity on the interaction between RBD and the cell receptor ACE2. In conclusion, our data have provided crucial information for understanding the mechanism of SARS-CoV-2 resistance to LCB1 and will guide the design strategy of novel LCB1-based antivirals against divergent VOCs and evolutionary mutants.
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Asghar A, Imran HM, Bano N, Maalik S, Mushtaq S, Hussain A, Varjani S, Aleya L, Iqbal HMN, Bilal M. SARS-COV-2/COVID-19: scenario, epidemiology, adaptive mutations, and environmental factors. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:69117-69136. [PMID: 35947257 PMCID: PMC9363873 DOI: 10.1007/s11356-022-22333-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
The coronavirus pandemic of 2019 has already exerted an enormous impact. For over a year, the worldwide pandemic has ravaged the whole globe, with approximately 250 million verified human infection cases and a mortality rate surpassing 4 million. While the genetic makeup of the related pathogen (SARS-CoV-2) was identified, many unknown facets remain a mystery, comprising the virus's origin and evolutionary trend. There were many rumors that SARS-CoV-2 was human-borne and its evolution was predicted many years ago, but scientific investigation proved them wrong and concluded that bats might be the origin of SARS-CoV-2 and pangolins act as intermediary species to transmit the virus from bats to humans. Airborne droplets were found to be the leading cause of human-to-human transmission of this virus, but later studies showed that contaminated surfaces and other environmental factors are also involved in its transmission. The evolution of different SARS-CoV-2 variants worsens the condition and has become a challenge to overcome this pandemic. The emergence of COVID-19 is still a mystery, and scientists are unable to explain the exact origin of SARS-CoV-2. This review sheds light on the possible origin of SARS-CoV-2, its transmission, and the key factors that worsen the situation.
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Affiliation(s)
- Asma Asghar
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Hafiz Muhammad Imran
- Department of Biochemistry, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Naheed Bano
- Department of Fisheries & Aquaculture, MNS-University of Agriculture, Multan, Pakistan
| | - Sadia Maalik
- Department of Zoology, Government College Women University, Sialkot, Pakistan
| | - Sajida Mushtaq
- Department of Zoology, Government College Women University, Sialkot, Pakistan
| | - Asim Hussain
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Sunita Varjani
- Gujarat Pollution Control Board, Gandhinagar, 382 010, Gujarat, India
| | - Lotfi Aleya
- Chrono-Environment Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, Besançon, France
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, 64849, Monterrey, Mexico
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, China.
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Wang M, Chang W, Zhang L, Zhang Y. Pyroptotic cell death in SARS-CoV-2 infection: revealing its roles during the immunopathogenesis of COVID-19. Int J Biol Sci 2022; 18:5827-5848. [PMID: 36263178 PMCID: PMC9576507 DOI: 10.7150/ijbs.77561] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/10/2022] [Indexed: 01/12/2023] Open
Abstract
The rapid dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), remains a global public health emergency. The host immune response to SARS-CoV-2 plays a key role in COVID-19 pathogenesis. SARS-CoV-2 can induce aberrant and excessive immune responses, leading to cytokine storm syndrome, autoimmunity, lymphopenia, neutrophilia and dysfunction of monocytes and macrophages. Pyroptosis, a proinflammatory form of programmed cell death, acts as a host defense mechanism against infections. Pyroptosis deprives the replicative niche of SARS-CoV-2 by inducing the lysis of infected cells and exposing the virus to extracellular immune attack. Notably, SARS-CoV-2 has evolved sophisticated mechanisms to hijack this cell death mode for its own survival, propagation and shedding. SARS-CoV-2-encoded viral products act to modulate various key components in the pyroptosis pathways, including inflammasomes, caspases and gasdermins. SARS-CoV-2-induced pyroptosis contriubtes to the development of COVID-19-associated immunopathologies through leakage of intracellular contents, disruption of immune system homeostasis or exacerbation of inflammation. Therefore, pyroptosis has emerged as an important mechanism involved in COVID-19 immunopathogenesis. However, the entangled links between pyroptosis and SARS-CoV-2 pathogenesis lack systematic clarification. In this review, we briefly summarize the characteristics of SARS-CoV-2 and COVID-19-related immunopathologies. Moreover, we present an overview of the interplay between SARS-CoV-2 infection and pyroptosis and highlight recent research advances in the understanding of the mechanisms responsible for the implication of the pyroptosis pathways in COVID-19 pathogenesis, which will provide informative inspirations and new directions for further investigation and clinical practice. Finally, we discuss the potential value of pyroptosis as a therapeutic target in COVID-19. An in-depth discussion of the underlying mechanisms of COVID-19 pathogenesis will be conducive to the identification of potential therapeutic targets and the exploration of effective treatment measures aimed at conquering SARS-CoV-2-induced COVID-19.
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Affiliation(s)
- Man Wang
- ✉ Corresponding author: Man Wang, Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 38 Dengzhou Road, Qingdao 266021, China. Tel.: +86-532-82991791; E-mail address:
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Li Q, Humphries F, Girardin RC, Wallace A, Ejemel M, Amcheslavsky A, McMahon CT, Schiller ZA, Ma Z, Cruz J, Dupuis AP, Payne AF, Maryam A, Yilmaz NK, McDonough KA, Pierce BG, Schiffer CA, Kruse AC, Klempner MS, Cavacini LA, Fitzgerald KA, Wang Y. Mucosal nanobody IgA as inhalable and affordable prophylactic and therapeutic treatment against SARS-CoV-2 and emerging variants. Front Immunol 2022; 13:995412. [PMID: 36172366 PMCID: PMC9512078 DOI: 10.3389/fimmu.2022.995412] [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: 07/15/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
Anti-COVID antibody therapeutics have been developed but not widely used due to their high cost and escape of neutralization from the emerging variants. Here, we describe the development of VHH-IgA1.1, a nanobody IgA fusion molecule as an inhalable, affordable and less invasive prophylactic and therapeutic treatment against SARS-CoV-2 Omicron variants. VHH-IgA1.1 recognizes a conserved epitope of SARS-CoV-2 spike protein Receptor Binding Domain (RBD) and potently neutralizes major global SARS-CoV-2 variants of concern (VOC) including the Omicron variant and its sub lineages BA.1.1, BA.2 and BA.2.12.1. VHH-IgA1.1 is also much more potent against Omicron variants as compared to an IgG Fc fusion construct, demonstrating the importance of IgA mediated mucosal protection for Omicron infection. Intranasal administration of VHH-IgA1.1 prior to or after challenge conferred significant protection from severe respiratory disease in K18-ACE2 transgenic mice infected with SARS-CoV-2 VOC. More importantly, for cost-effective production, VHH-IgA1.1 produced in Pichia pastoris had comparable potency to mammalian produced antibodies. Our study demonstrates that intranasal administration of affordably produced VHH-IgA fusion protein provides effective mucosal immunity against infection of SARS-CoV-2 including emerging variants.
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Affiliation(s)
- Qi Li
- MassBiologics, University of Massachusetts Chan Medical School, Boston, MA, United States
| | - Fiachra Humphries
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Roxie C. Girardin
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Aaron Wallace
- MassBiologics, University of Massachusetts Chan Medical School, Boston, MA, United States
| | - Monir Ejemel
- MassBiologics, University of Massachusetts Chan Medical School, Boston, MA, United States
| | - Alla Amcheslavsky
- MassBiologics, University of Massachusetts Chan Medical School, Boston, MA, United States
| | - Conor T. McMahon
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
| | - Zachary A. Schiller
- MassBiologics, University of Massachusetts Chan Medical School, Boston, MA, United States
| | - Zepei Ma
- MassBiologics, University of Massachusetts Chan Medical School, Boston, MA, United States
| | - John Cruz
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Alan P. Dupuis
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Anne F. Payne
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Arooma Maryam
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | | | - Brian G. Pierce
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, United States
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Andrew C. Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
| | - Mark S. Klempner
- MassBiologics, University of Massachusetts Chan Medical School, Boston, MA, United States
| | - Lisa A. Cavacini
- MassBiologics, University of Massachusetts Chan Medical School, Boston, MA, United States
- *Correspondence: Yang Wang, ; Katherine A. Fitzgerald, ; Lisa A. Cavacini,
| | - Katherine A. Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States
- *Correspondence: Yang Wang, ; Katherine A. Fitzgerald, ; Lisa A. Cavacini,
| | - Yang Wang
- MassBiologics, University of Massachusetts Chan Medical School, Boston, MA, United States
- *Correspondence: Yang Wang, ; Katherine A. Fitzgerald, ; Lisa A. Cavacini,
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da Silva SJR, do Nascimento JCF, Germano Mendes RP, Guarines KM, Targino Alves da Silva C, da Silva PG, de Magalhães JJF, Vigar JRJ, Silva-Júnior A, Kohl A, Pardee K, Pena L. Two Years into the COVID-19 Pandemic: Lessons Learned. ACS Infect Dis 2022; 8:1758-1814. [PMID: 35940589 PMCID: PMC9380879 DOI: 10.1021/acsinfecdis.2c00204] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and virulent human-infecting coronavirus that emerged in late December 2019 in Wuhan, China, causing a respiratory disease called coronavirus disease 2019 (COVID-19), which has massively impacted global public health and caused widespread disruption to daily life. The crisis caused by COVID-19 has mobilized scientists and public health authorities across the world to rapidly improve our knowledge about this devastating disease, shedding light on its management and control, and spawned the development of new countermeasures. Here we provide an overview of the state of the art of knowledge gained in the last 2 years about the virus and COVID-19, including its origin and natural reservoir hosts, viral etiology, epidemiology, modes of transmission, clinical manifestations, pathophysiology, diagnosis, treatment, prevention, emerging variants, and vaccines, highlighting important differences from previously known highly pathogenic coronaviruses. We also discuss selected key discoveries from each topic and underline the gaps of knowledge for future investigations.
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Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Jessica Catarine Frutuoso do Nascimento
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Renata Pessôa Germano Mendes
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Klarissa Miranda Guarines
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Caroline Targino Alves da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Poliana Gomes da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Jurandy Júnior Ferraz de Magalhães
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Virology, Pernambuco State Central Laboratory (LACEN/PE), 52171-011 Recife, Pernambuco, Brazil.,University of Pernambuco (UPE), Serra Talhada Campus, 56909-335 Serra Talhada, Pernambuco, Brazil.,Public Health Laboratory of the XI Regional Health, 56912-160 Serra Talhada, Pernambuco, Brazil
| | - Justin R J Vigar
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Abelardo Silva-Júnior
- Institute of Biological and Health Sciences, Federal University of Alagoas (UFAL), 57072-900 Maceió, Alagoas, Brazil
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, United Kingdom
| | - Keith Pardee
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada.,Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Lindomar Pena
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
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SARS-CoV-2 Infections in Vaccinated and Unvaccinated Populations in Camp Lemonnier, Djibouti, from April 2020 to January 2022. Viruses 2022; 14:v14091918. [PMID: 36146724 PMCID: PMC9505681 DOI: 10.3390/v14091918] [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: 07/29/2022] [Revised: 08/24/2022] [Accepted: 08/28/2022] [Indexed: 12/12/2022] Open
Abstract
The global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the disparity between developed and developing countries for infectious disease surveillance and the sequencing of pathogen genomes. The majority of SARS-CoV-2 sequences published are from Europe, North America, and Asia. Between April 2020 and January 2022, 795 SARS-CoV-2-positive nares swabs from individuals in the U.S. Navy installation Camp Lemonnier, Djibouti, were collected, sequenced, and analyzed. In this study, we described the results of genomic sequencing and analysis for 589 samples, the first published viral sequences for Djibouti, including 196 cases of vaccine breakthrough infections. This study contributes to the knowledge base of circulating SARS-CoV-2 lineages in the under-sampled country of Djibouti, where only 716 total genome sequences are available at time of publication. Our analysis resulted in the detection of circulating variants of concern, mutations of interest in lineages in which those mutations are not common, and emerging spike mutations.
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Promotion of neutralizing antibody-independent immunity to wild-type and SARS-CoV-2 variants of concern using an RBD-Nucleocapsid fusion protein. Nat Commun 2022; 13:4831. [PMID: 35977933 PMCID: PMC9382605 DOI: 10.1038/s41467-022-32547-y] [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: 04/15/2022] [Accepted: 08/05/2022] [Indexed: 11/20/2022] Open
Abstract
Both T cells and B cells have been shown to be generated after infection with SARS-CoV-2 yet protocols or experimental models to study one or the other are less common. Here, we generate a chimeric protein (SpiN) that comprises the receptor binding domain (RBD) from Spike (S) and the nucleocapsid (N) antigens from SARS-CoV-2. Memory CD4+ and CD8+ T cells specific for SpiN could be detected in the blood of both individuals vaccinated with Coronavac SARS-CoV-2 vaccine and COVID-19 convalescent donors. In mice, SpiN elicited a strong IFN-γ response by T cells and high levels of antibodies to the inactivated virus, but not detectable neutralizing antibodies (nAbs). Importantly, immunization of Syrian hamsters and the human Angiotensin Convertase Enzyme-2-transgenic (K18-ACE-2) mice with Poly ICLC-adjuvanted SpiN promotes robust resistance to the wild type SARS-CoV-2, as indicated by viral load, lung inflammation, clinical outcome and reduction of lethality. The protection induced by SpiN was ablated by depletion of CD4+ and CD8+ T cells and not transferred by antibodies from vaccinated mice. Finally, vaccination with SpiN also protects the K18-ACE-2 mice against infection with Delta and Omicron SARS-CoV-2 isolates. Hence, vaccine formulations that elicit effector T cells specific for the N and RBD proteins may be used to improve COVID-19 vaccines and potentially circumvent the immune escape by variants of concern. Protection against SARS-CoV-2 infection involves T cell and B cell responses but only studying one or the other has proved difficult. Here the authors immunise with a fusion protein construct of N and RBD proteins from SARS-CoV-2 and find that this promotes protection in animal models preferentially via T cells.
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43
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Zhu C, Lee JY, Woo JZ, Xu L, Nguyenla X, Yamashiro LH, Ji F, Biering SB, Van Dis E, Gonzalez F, Fox D, Wehri E, Rustagi A, Pinsky BA, Schaletzky J, Blish CA, Chiu C, Harris E, Sadreyev RI, Stanley S, Kauppinen S, Rouskin S, Näär AM. An intranasal ASO therapeutic targeting SARS-CoV-2. Nat Commun 2022; 13:4503. [PMID: 35922434 PMCID: PMC9349213 DOI: 10.1038/s41467-022-32216-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/18/2022] [Indexed: 12/13/2022] Open
Abstract
The COVID-19 pandemic is exacting an increasing toll worldwide, with new SARS-CoV-2 variants emerging that exhibit higher infectivity rates and that may partially evade vaccine and antibody immunity. Rapid deployment of non-invasive therapeutic avenues capable of preventing infection by all SARS-CoV-2 variants could complement current vaccination efforts and help turn the tide on the COVID-19 pandemic. Here, we describe a novel therapeutic strategy targeting the SARS-CoV-2 RNA using locked nucleic acid antisense oligonucleotides (LNA ASOs). We identify an LNA ASO binding to the 5′ leader sequence of SARS-CoV-2 that disrupts a highly conserved stem-loop structure with nanomolar efficacy in preventing viral replication in human cells. Daily intranasal administration of this LNA ASO in the COVID-19 mouse model potently suppresses viral replication (>80-fold) in the lungs of infected mice. We find that the LNA ASO is efficacious in countering all SARS-CoV-2 “variants of concern” tested both in vitro and in vivo. Hence, inhaled LNA ASOs targeting SARS-CoV-2 represents a promising therapeutic approach to reduce or prevent transmission and decrease severity of COVID-19 in infected individuals. LNA ASOs are chemically stable and can be flexibly modified to target different viral RNA sequences and could be stockpiled for future coronavirus pandemics. Despite approved vaccines and anti-virals to prevent and treat SARS-CoV-2 infection, there is a need for further development of efficient antiviral therapeutic strategy. Here, Zhu et al. develop locked nucleic acid antisense oligonucleotides (LNA ASOs) targeting the 5’ leader sequence of SARS-CoV-2 RNA to interfere with replication of wildtype virus and variants of concern. Daily intranasal administration in K18-hACE2 humanized mice suppresses viral infection in lung.
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Affiliation(s)
- Chi Zhu
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Justin Y Lee
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Jia Z Woo
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Lei Xu
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Xammy Nguyenla
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Livia H Yamashiro
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Scott B Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Erik Van Dis
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, USA
| | - Federico Gonzalez
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Douglas Fox
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Eddie Wehri
- The Henry Wheeler Center for Emerging and Neglected Diseases, University of California, Berkeley, CA, USA
| | - Arjun Rustagi
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | - Benjamin A Pinsky
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia Schaletzky
- The Henry Wheeler Center for Emerging and Neglected Diseases, University of California, Berkeley, CA, USA
| | - Catherine A Blish
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | - Charles Chiu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Sarah Stanley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, USA
| | - Sakari Kauppinen
- Center for RNA Medicine, Aalborg University, Copenhagen, Denmark
| | - Silvi Rouskin
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Anders M Näär
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, CA, USA. .,Innovative Genomics Institute, University of California, Berkeley, CA, USA.
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Solanki K, Rajpoot S, Kumar A, J Zhang KY, Ohishi T, Hirani N, Wadhonkar K, Patidar P, Pan Q, Baig MS. Structural analysis of spike proteins from SARS-CoV-2 variants of concern highlighting their functional alterations. Future Virol 2022. [PMID: 35935449 PMCID: PMC9345306 DOI: 10.2217/fvl-2022-0003] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 07/22/2022] [Indexed: 12/15/2022]
Abstract
Aim: Mutations in the SARS-CoV-2 spike (S) protein have dramatically changed the transmissibility and pathogenicity of the virus. Therefore, we studied the binding affinity of Omicron spike-receptor binding domain (S-RBD) with human ACE2 receptor. Materials & methods: We used pyDockWEB and HADDOCK 2.4 docking for our study. Results: Computational docking indicated higher binding affinity of Omicron S-RBD as compared with wild-type SARS-CoV-2 and Delta S-RBD with ACE2. Interface analysis suggested four mutated residues of Omicron S-RBD for its enhanced binding. We also showed decreased binding affinity of Omicron and Delta S-RBDs with monoclonal antibodies. Conclusion: Compared with wild-type SARS-CoV-2, Omicron S-RBD exhibit higher binding with ACE2 and lower affinity against monoclonal antibodies.
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Affiliation(s)
- Kundan Solanki
- Department of Biosciences & Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Sajjan Rajpoot
- Department of Biosciences & Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Ashutosh Kumar
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Tomokazu Ohishi
- Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, Numazu-Shi, Shizuoka, 410-0301, Japan
| | - Nik Hirani
- MRC Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH164TJ, UK
| | - Khandu Wadhonkar
- Department of Biosciences & Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Pramod Patidar
- Department of Biosciences & Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Qiuwei Pan
- Department of Gastroenterology & Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Mirza S Baig
- Department of Biosciences & Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
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45
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da Silva ES, Kohnen M, Gilson G, Staub T, Arendt V, Hilger C, Servais JY, Charpentier E, Domingues O, Snoeck CJ, Ollert M, Seguin-Devaux C, Perez-Bercoff D. Pre-Omicron Vaccine Breakthrough Infection Induces Superior Cross-Neutralization against SARS-CoV-2 Omicron BA.1 Compared to Infection Alone. Int J Mol Sci 2022; 23:7675. [PMID: 35887023 PMCID: PMC9320437 DOI: 10.3390/ijms23147675] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 02/05/2023] Open
Abstract
SARS-CoV-2 variants raise concern because of their high transmissibility and their ability to evade neutralizing antibodies elicited by prior infection or by vaccination. Here, we compared the neutralizing abilities of sera from 70 unvaccinated COVID-19 patients infected before the emergence of variants of concern (VOCs) and of 16 vaccine breakthrough infection (BTI) cases infected with Gamma or Delta against the ancestral B.1 strain, the Gamma, Delta and Omicron BA.1 VOCs using live virus. We further determined antibody levels against the Nucleocapsid (N) and full Spike proteins, the receptor-binding domain (RBD) and the N-terminal domain (NTD) of the Spike protein. Convalescent sera featured considerable variability in the neutralization of B.1 and in the cross-neutralization of different strains. Their neutralizing capacity moderately correlated with antibody levels against the Spike protein and the RBD. All but one convalescent serum failed to neutralize Omicron BA.1. Overall, convalescent sera from patients with moderate disease had higher antibody levels and displayed a higher neutralizing ability against all strains than patients with mild or severe forms of the disease. The sera from BTI cases fell into one of two categories: half the sera had a high neutralizing activity against the ancestral B.1 strain as well as against the infecting strain, while the other half had no or a very low neutralizing activity against all strains. Although antibody levels against the spike protein and the RBD were lower in BTI sera than in unvaccinated convalescent sera, most neutralizing sera also retained partial neutralizing activity against Omicron BA.1, suggestive of a better cross-neutralization and higher affinity of vaccine-elicited antibodies over virus-induced antibodies. Accordingly, the IC50: antibody level ratios were comparable for BTI and convalescent sera, but remained lower in the neutralizing convalescent sera from patients with moderate disease than in BTI sera. The neutralizing activity of BTI sera was strongly correlated with antibodies against the Spike protein and the RBD. Together, these findings highlight qualitative differences in antibody responses elicited by infection in vaccinated and unvaccinated individuals. They further indicate that breakthrough infection with a pre-Omicron variant boosts immunity and induces cross-neutralizing antibodies against different strains, including Omicron BA.1.
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Affiliation(s)
- Eveline Santos da Silva
- HIV Clinical and Translational Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (C.S.-D.)
| | - Michel Kohnen
- Centre Hospitalier de Luxembourg, 4 rue Ernest Barblé, L-1210 Luxembourg, Luxembourg; (M.K.); (G.G.); (T.S.); (V.A.)
| | - Georges Gilson
- Centre Hospitalier de Luxembourg, 4 rue Ernest Barblé, L-1210 Luxembourg, Luxembourg; (M.K.); (G.G.); (T.S.); (V.A.)
| | - Therese Staub
- Centre Hospitalier de Luxembourg, 4 rue Ernest Barblé, L-1210 Luxembourg, Luxembourg; (M.K.); (G.G.); (T.S.); (V.A.)
| | - Victor Arendt
- Centre Hospitalier de Luxembourg, 4 rue Ernest Barblé, L-1210 Luxembourg, Luxembourg; (M.K.); (G.G.); (T.S.); (V.A.)
| | - Christiane Hilger
- Molecular and Translational Allergology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg;
| | - Jean-Yves Servais
- HIV Clinical and Translational Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (C.S.-D.)
| | - Emilie Charpentier
- Clinical and Applied Virology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.C.); (C.J.S.)
| | - Olivia Domingues
- Allergy and Clinical Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (O.D.); (M.O.)
| | - Chantal J. Snoeck
- Clinical and Applied Virology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.C.); (C.J.S.)
| | - Markus Ollert
- Allergy and Clinical Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (O.D.); (M.O.)
| | - Carole Seguin-Devaux
- HIV Clinical and Translational Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (C.S.-D.)
| | - Danielle Perez-Bercoff
- HIV Clinical and Translational Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (C.S.-D.)
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46
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Alexandre M, Marlin R, Prague M, Coleon S, Kahlaoui N, Cardinaud S, Naninck T, Delache B, Surenaud M, Galhaut M, Dereuddre-Bosquet N, Cavarelli M, Maisonnasse P, Centlivre M, Lacabaratz C, Wiedemann A, Zurawski S, Zurawski G, Schwartz O, Sanders RW, Le Grand R, Levy Y, Thiébaut R. Modelling the response to vaccine in non-human primates to define SARS-CoV-2 mechanistic correlates of protection. eLife 2022; 11:75427. [PMID: 35801637 PMCID: PMC9282856 DOI: 10.7554/elife.75427] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 06/22/2022] [Indexed: 11/29/2022] Open
Abstract
The definition of correlates of protection is critical for the development of next-generation SARS-CoV-2 vaccine platforms. Here, we propose a model-based approach for identifying mechanistic correlates of protection based on mathematical modelling of viral dynamics and data mining of immunological markers. The application to three different studies in non-human primates evaluating SARS-CoV-2 vaccines based on CD40-targeting, two-component spike nanoparticle and mRNA 1273 identifies and quantifies two main mechanisms that are a decrease of rate of cell infection and an increase in clearance of infected cells. Inhibition of RBD binding to ACE2 appears to be a robust mechanistic correlate of protection across the three vaccine platforms although not capturing the whole biological vaccine effect. The model shows that RBD/ACE2 binding inhibition represents a strong mechanism of protection which required significant reduction in blocking potency to effectively compromise the control of viral replication.
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Affiliation(s)
- Marie Alexandre
- Department of Public Health, Inserm Bordeaux Population Health Research Centre, University of Bordeaux, Inria SISTM, UMR 1219, Bordeaux, France
| | - Romain Marlin
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Mélanie Prague
- Department of Public Health, Inserm Bordeaux Population Health Research Centre, University of Bordeaux, Inria SISTM, UMR 1219, Bordeaux, France
| | - Severin Coleon
- Vaccine Research Institute, Inserm U955, Créteil, France
| | - Nidhal Kahlaoui
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | | | - Thibaut Naninck
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Benoit Delache
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | | | - Mathilde Galhaut
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Nathalie Dereuddre-Bosquet
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Mariangela Cavarelli
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Pauline Maisonnasse
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | | | | | | | - Sandra Zurawski
- Baylor Scott and White Research Institute, Dallas, United States
| | - Gerard Zurawski
- Baylor Scott and White Research Institute, Dallas, United States
| | | | - Rogier W Sanders
- Department of Medical Microbiology, University of Amsterdam, Amsterdam, Netherlands
| | - Roger Le Grand
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Yves Levy
- Vaccine Research Institute, Inserm U955, Créteil, France
| | - Rodolphe Thiébaut
- Department of Public Health, Inserm Bordeaux Population Health Research Centre, University of Bordeaux, Inria SISTM, UMR 1219, Bordeaux, France
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47
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Zhu Y, Dong X, Liu N, Wu T, Chong H, Lei X, Ren L, Wang J, He Y. SARS-CoV-2 fusion-inhibitory lipopeptides maintain high potency against divergent variants of concern (VOCs) including Omicron. Emerg Microbes Infect 2022; 11:1819-1827. [PMID: 35786417 PMCID: PMC9310806 DOI: 10.1080/22221751.2022.2098060] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The emergence of SARS-CoV-2 Omicron and other variants of concern (VOCs) has brought huge challenges to control the COVID-19 pandemic, calling for urgent development of effective vaccines and therapeutic drugs. In this study, we focused on characterizing the impacts of divergent VOCs on the antiviral activity of lipopeptide-based fusion inhibitors that we previously developed. First, we found that pseudoviruses bearing the S proteins of five VOCs (Alpha, Beta, Gamma, Delta, and Omicron) and one variant of interest (Lambda) exhibited greatly decreased infectivity relative to the wild-type (WT) strain or single D614G mutant, especially the Omicron pseudovirus. Differently, the most of variants exhibited an S protein with significantly enhanced cell fusion activity, whereas the S protein of Omicron still mediated decreased cell–cell fusion. Next, we verified that two lipopeptide-based fusion inhibitors, IPB02V3 and IPB24, maintained the highly potent activities in inhibiting various S proteins-driven cell fusion and pseudovirus infection. Surprisingly, both IPB02V3 and IPB24 lipopeptides displayed greatly increased potencies against the infection of authentic Omicron strain relative to the WT virus. The results suggest that Omicron variant evolves with a reduced cell fusion capacity and is more sensitive to the inhibition of fusion-inhibitory lipopeptides; thus, IPB02V3 and IPB24 can be further developed as potent, broad-spectrum antivirals for combating Omicron and the potential future outbreak of other emerging variants.
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Affiliation(s)
- Yuanmei Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xiaojing Dong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Nian Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Tong Wu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Huihui Chong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xiaobo Lei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Lili Ren
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yuxian He
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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48
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Sun H, Xu J, Zhang G, Han J, Hao M, Chen Z, Fang T, Chi X, Yu C. Developing Pseudovirus-Based Neutralization Assay against Omicron-Included SARS-CoV-2 Variants. Viruses 2022; 14:v14061332. [PMID: 35746803 PMCID: PMC9231177 DOI: 10.3390/v14061332] [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: 04/05/2022] [Revised: 06/06/2022] [Accepted: 06/16/2022] [Indexed: 02/07/2023] Open
Abstract
The global spread of SARS-CoV-2 and its variants poses a serious threat to human health worldwide. Recently, the emergence of Omicron has presented a new challenge to the prevention and control of the COVID-19 pandemic. A convenient and reliable in vitro neutralization assay is an important method for validating the efficiency of antibodies, vaccines, and other potential drugs. Here, we established an effective assay based on a pseudovirus carrying a full-length spike (S) protein of SARS-CoV-2 variants in the HIV-1 backbone, with a luciferase reporter gene inserted into the non-replicate pseudovirus genome. The key parameters for packaging the pseudovirus were optimized, including the ratio of the S protein expression plasmids to the HIV backbone plasmids and the collection time for the Alpha, Beta, Gamma, Kappa, and Omicron pseudovirus particles. The pseudovirus neutralization assay was validated using several approved or developed monoclonal antibodies, underscoring that Omicron can escape some neutralizing antibodies, such as REGN10987 and REGN10933, while S309 and ADG-2 still function with reduced neutralization capability. The neutralizing capacity of convalescent plasma from COVID-19 convalescent patients in Wuhan was tested against these pseudoviruses, revealing the immune evasion of Omicron. Our work established a practical pseudovirus-based neutralization assay for SARS-CoV-2 variants, which can be conducted safely under biosafety level-2 (BSL-2) conditions, and this assay will be a promising tool for studying and characterizing vaccines and therapeutic candidates against Omicron-included SARS-CoV-2 variants.
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49
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Faraji SN, Raee MJ, Hashemi SMA, Daryabor G, Tabrizi R, Dashti FS, Behboudi E, Heidarnejad K, Nowrouzi-Sohrabi P, Hatam G. Human interaction targets of SARS-COV-2 spike protein: A systematic review. EUR J INFLAMM 2022. [PMCID: PMC9160582 DOI: 10.1177/1721727x221095382] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Objectives: The development of effective targeted therapy and drug-design approaches against the SARS-CoV-2 is a universal health priority. Therefore, it is important to assess possible therapeutic strategies against SARS-CoV-2 via its most interaction targets. The present study aimed to perform a systematic review on clinical and experimental investigations regarding SARS-COV-2 interaction targets for human cell entry. Methods: A systematic search using relevant MeSH terms and keywords was performed in PubMed, Scopus, Embase, and Web of Science (ISI) databases up to July 2021. Two reviewers independently assessed the eligibility of the studies, extracted the data, and evaluated the methodological quality of the included studies. Additionally, a narrative synthesis was done as a qualitative method for data gathering and synthesis of each outcome measure. Results: A total of 5610 studies were identified, and 128 articles were included in the systematic review. Based on the results, spike antigen was the only interaction protein from SARS-CoV-2. However, the interaction proteins from humans varied including different spike receptors and several cleavage enzymes. The most common interactions of the spike protein of SARS-CoV-2 for cell entry were ACE2 (entry receptor) and TMPRSS2 (for spike priming). A lot of published studies have mainly focused on the ACE2 receptor followed by the TMPRSS family and furin. Based on the results, ACE2 polymorphisms as well as spike RBD mutations affected the SARS-CoV-2 binding affinity. Conclusion: The included studies shed more light on SARS-CoV-2 cellular entry mechanisms and detailed interactions, which could enhance the understanding of SARS-CoV-2 pathogenesis and the development of new and comprehensive therapeutic approaches.
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Affiliation(s)
- Seyed Nooreddin Faraji
- School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohamad Javad Raee
- Center for Nanotechnology in Drug Delivery, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Mohamad Ali Hashemi
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Microbiology, Golestan University of Medical Sciences, Gorgan, Iran
| | - Gholamreza Daryabor
- Autoimmune Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Tabrizi
- Non-communicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Fateme Sadat Dashti
- Research Center for Food Hygiene and Safety, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Emad Behboudi
- Department of Microbiology, Golestan University of Medical Sciences, Gorgan, Iran
| | - Kamran Heidarnejad
- Recombinant Antibody Laboratory, Department of Immunology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Peyman Nowrouzi-Sohrabi
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Gholamreza Hatam
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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Greaney AJ, Eguia RT, Starr TN, Khan K, Franko N, Logue JK, Lord SM, Speake C, Chu HY, Sigal A, Bloom JD. The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. PLoS Pathog 2022; 18:e1010592. [PMID: 35767821 PMCID: PMC9275729 DOI: 10.1371/journal.ppat.1010592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/12/2022] [Accepted: 05/15/2022] [Indexed: 12/23/2022] Open
Abstract
Exposure histories to SARS-CoV-2 variants and vaccinations will shape the specificity of antibody responses. To understand the specificity of Delta-elicited antibody immunity, we characterize the polyclonal antibody response elicited by primary or mRNA vaccine-breakthrough Delta infections. Both types of infection elicit a neutralizing antibody response focused heavily on the receptor-binding domain (RBD). We use deep mutational scanning to show that mutations to the RBD's class 1 and class 2 epitopes, including sites 417, 478, and 484-486 often reduce binding of these Delta-elicited antibodies. The anti-Delta antibody response is more similar to that elicited by early 2020 viruses than the Beta variant, with mutations to the class 1 and 2, but not class 3 epitopes, having the largest effects on polyclonal antibody binding. In addition, mutations to the class 1 epitope (e.g., K417N) tend to have larger effects on antibody binding and neutralization in the Delta spike than in the D614G spike, both for vaccine- and Delta-infection-elicited antibodies. These results help elucidate how the antigenic impacts of SARS-CoV-2 mutations depend on exposure history.
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Affiliation(s)
- Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, Washington, United States of America
| | - Rachel T. Eguia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Khadija Khan
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - Nicholas Franko
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Jennifer K. Logue
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Sandra M. Lord
- Center for Interventional Immunology, Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States of America
| | - Cate Speake
- Center for Interventional Immunology, Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States of America
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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