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Wongnak R, Brindha S, Oba M, Yoshizue T, Islam MD, Islam MM, Takemae H, Mizutani T, Kuroda Y. Non-Glycosylated SARS-CoV-2 Omicron BA.5 Receptor Binding Domain (RBD) with a Native-like Conformation Induces a Robust Immune Response with Potent Neutralization in a Mouse Model. Molecules 2024; 29:2676. [PMID: 38893549 PMCID: PMC11173568 DOI: 10.3390/molecules29112676] [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: 05/02/2024] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
The Omicron BA.5 variant of SARS-CoV-2 is known for its high transmissibility and its capacity to evade immunity provided by vaccine protection against the (original) Wuhan strain. In our prior research, we successfully produced the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein in an E. coli expression system. Extensive biophysical characterization indicated that, even without glycosylation, the RBD maintained native-like conformational and biophysical properties. The current study explores the immunogenicity and neutralization capacity of the E. coli-expressed Omicron BA.5 RBD using a mouse model. Administration of three doses of the RBD without any adjuvant elicited high titer antisera of up to 7.3 × 105 and up to 1.6 × 106 after a booster shot. Immunization with RBD notably enhanced the population of CD44+CD62L+ T cells, indicating the generation of T cell memory. The in vitro assays demonstrated the antisera's protective efficacy through significant inhibition of the interaction between SARS-CoV-2 and its human receptor, ACE2, and through potent neutralization of a pseudovirus. These findings underscore the potential of our E. coli-expressed RBD as a viable vaccine candidate against the Omicron variant of SARS-CoV-2.
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Affiliation(s)
- Rawiwan Wongnak
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Nakamachi 2-24-16, Tokyo 184-8588, Japan; (R.W.); (S.B.); (T.Y.); (M.D.I.)
| | - Subbaian Brindha
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Nakamachi 2-24-16, Tokyo 184-8588, Japan; (R.W.); (S.B.); (T.Y.); (M.D.I.)
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan; (M.O.); (H.T.); (T.M.)
| | - Mami Oba
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan; (M.O.); (H.T.); (T.M.)
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-Cho, Fuchu-shi 183-8509, Japan
| | - Takahiro Yoshizue
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Nakamachi 2-24-16, Tokyo 184-8588, Japan; (R.W.); (S.B.); (T.Y.); (M.D.I.)
| | - Md. Din Islam
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Nakamachi 2-24-16, Tokyo 184-8588, Japan; (R.W.); (S.B.); (T.Y.); (M.D.I.)
| | - M. Monirul Islam
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh;
| | - Hitoshi Takemae
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan; (M.O.); (H.T.); (T.M.)
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-Cho, Fuchu-shi 183-8509, Japan
| | - Tetsuya Mizutani
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan; (M.O.); (H.T.); (T.M.)
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-Cho, Fuchu-shi 183-8509, Japan
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Nakamachi 2-24-16, Tokyo 184-8588, Japan; (R.W.); (S.B.); (T.Y.); (M.D.I.)
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan; (M.O.); (H.T.); (T.M.)
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Hong W, Lei H, Peng D, Huang Y, He C, Yang J, Zhou Y, Liu J, Pan X, Que H, Alu A, Chen L, Ai J, Qin F, Wang B, Ao D, Zeng Z, Hao Y, Zhang Y, Huang X, Ye C, Fu M, He X, Bi Z, Han X, Luo M, Hu H, Cheng W, Dong H, Lei J, Chen L, Zhou X, Wang W, Lu G, Shen G, Yang L, Yang J, Li J, Wang Z, Song X, Sun Q, Lu S, Wang Y, Cheng P, Wei X. A chimeric adenovirus-vectored vaccine based on Beta spike and Delta RBD confers a broad-spectrum neutralization against Omicron-included SARS-CoV-2 variants. MedComm (Beijing) 2024; 5:e539. [PMID: 38680520 PMCID: PMC11055958 DOI: 10.1002/mco2.539] [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: 11/23/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 05/01/2024] Open
Abstract
Urgent research into innovative severe acute respiratory coronavirus-2 (SARS-CoV-2) vaccines that may successfully prevent various emerging emerged variants, particularly the Omicron variant and its subvariants, is necessary. Here, we designed a chimeric adenovirus-vectored vaccine named Ad5-Beta/Delta. This vaccine was created by incorporating the receptor-binding domain from the Delta variant, which has the L452R and T478K mutations, into the complete spike protein of the Beta variant. Both intramuscular (IM) and intranasal (IN) vaccination with Ad5-Beta/Deta vaccine induced robust broad-spectrum neutralization against Omicron BA.5-included variants. IN immunization with Ad5-Beta/Delta vaccine exhibited superior mucosal immunity, manifested by higher secretory IgA antibodies and more tissue-resident memory T cells (TRM) in respiratory tract. The combination of IM and IN delivery of the Ad5-Beta/Delta vaccine was capable of synergically eliciting stronger systemic and mucosal immune responses. Furthermore, the Ad5-Beta/Delta vaccination demonstrated more effective boosting implications after two dosages of mRNA or subunit recombinant protein vaccine, indicating its capacity for utilization as a booster shot in the heterologous vaccination. These outcomes quantified Ad5-Beta/Delta vaccine as a favorable vaccine can provide protective immunity versus SARS-CoV-2 pre-Omicron variants of concern and BA.5-included Omicron subvariants.
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Ciubotariu II, Wilkes RP, Kattoor JJ, Christian EN, Carpi G, Kitchen A. Investigating the rise of Omicron variant through genomic surveillance of SARS-CoV-2 infections in a highly vaccinated university population. Microb Genom 2024; 10:001194. [PMID: 38334271 PMCID: PMC10926704 DOI: 10.1099/mgen.0.001194] [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: 11/08/2023] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
Novel variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to emerge as the coronavirus disease 2019 (COVID-19) pandemic extends into its fourth year. Understanding SARS-CoV-2 circulation in university populations is vital for effective interventions in higher education settings and will inform public health policy during pandemics. In this study, we generated 793 whole-genome sequences collected over an entire academic year in a university population in Indiana, USA. We clearly captured the rapidity with which Delta variant was wholly replaced by Omicron variant across the West Lafayette campus over the length of two academic semesters in a community with high vaccination rates. This mirrored the emergence of Omicron throughout the state of Indiana and the USA. Further, phylogenetic analyses demonstrated that there was a more diverse set of potential geographic origins for Omicron viruses introduction into campus when compared to Delta. Lastly, statistics indicated that there was a more significant role for international and out-of-state migration in the establishment of Omicron variants at Purdue. This surveillance workflow, coupled with viral genomic sequencing and phylogeographic analyses, provided critical insights into SARS-CoV-2 transmission dynamics and variant arrival.
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Affiliation(s)
- Ilinca I. Ciubotariu
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - Rebecca P. Wilkes
- Department of Comparative Pathobiology, Animal Disease Diagnostic Laboratory, Purdue University College of Veterinary Medicine, West Lafayette, Indiana 47907, USA
| | - Jobin J. Kattoor
- Department of Comparative Pathobiology, Animal Disease Diagnostic Laboratory, Purdue University College of Veterinary Medicine, West Lafayette, Indiana 47907, USA
| | - Erin N. Christian
- Department of Comparative Pathobiology, Animal Disease Diagnostic Laboratory, Purdue University College of Veterinary Medicine, West Lafayette, Indiana 47907, USA
| | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, Indiana 47907, USA
| | - Andrew Kitchen
- Department of Anthropology, University of Iowa, Iowa City, Iowa, USA
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Prakash S, Dhanushkodi NR, Zayou L, Ibraim IC, Quadiri A, Coulon PG, Tifrea DF, Suzer B, Shaik AM, Chilukuri A, Edwards RA, Singer M, Vahed H, Nesburn AB, Kuppermann BD, Ulmer JB, Gil D, Jones TM, BenMohamed L. Cross-protection induced by highly conserved human B, CD4 +, and CD8 + T-cell epitopes-based vaccine against severe infection, disease, and death caused by multiple SARS-CoV-2 variants of concern. Front Immunol 2024; 15:1328905. [PMID: 38318166 PMCID: PMC10839970 DOI: 10.3389/fimmu.2024.1328905] [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: 10/27/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024] Open
Abstract
Background The coronavirus disease 2019 (COVID-19) pandemic has created one of the largest global health crises in almost a century. Although the current rate of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections has decreased significantly, the long-term outlook of COVID-19 remains a serious cause of morbidity and mortality worldwide, with the mortality rate still substantially surpassing even that recorded for influenza viruses. The continued emergence of SARS-CoV-2 variants of concern (VOCs), including multiple heavily mutated Omicron sub-variants, has prolonged the COVID-19 pandemic and underscores the urgent need for a next-generation vaccine that will protect from multiple SARS-CoV-2 VOCs. Methods We designed a multi-epitope-based coronavirus vaccine that incorporated B, CD4+, and CD8+ T- cell epitopes conserved among all known SARS-CoV-2 VOCs and selectively recognized by CD8+ and CD4+ T-cells from asymptomatic COVID-19 patients irrespective of VOC infection. The safety, immunogenicity, and cross-protective immunity of this pan-variant SARS-CoV-2 vaccine were studied against six VOCs using an innovative triple transgenic h-ACE-2-HLA-A2/DR mouse model. Results The pan-variant SARS-CoV-2 vaccine (i) is safe , (ii) induces high frequencies of lung-resident functional CD8+ and CD4+ TEM and TRM cells , and (iii) provides robust protection against morbidity and virus replication. COVID-19-related lung pathology and death were caused by six SARS-CoV-2 VOCs: Alpha (B.1.1.7), Beta (B.1.351), Gamma or P1 (B.1.1.28.1), Delta (lineage B.1.617.2), and Omicron (B.1.1.529). Conclusion A multi-epitope pan-variant SARS-CoV-2 vaccine bearing conserved human B- and T- cell epitopes from structural and non-structural SARS-CoV-2 antigens induced cross-protective immunity that facilitated virus clearance, and reduced morbidity, COVID-19-related lung pathology, and death caused by multiple SARS-CoV-2 VOCs.
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Affiliation(s)
- Swayam Prakash
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Nisha R Dhanushkodi
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Latifa Zayou
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Izabela Coimbra Ibraim
- High Containment Facility, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Afshana Quadiri
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Pierre Gregoire Coulon
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Delia F Tifrea
- Department of Pathology and Laboratory Medicine, School of Medicine, the University of California Irvine, Irvine, CA, United States
| | - Berfin Suzer
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Amin Mohammed Shaik
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Amruth Chilukuri
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Robert A Edwards
- Department of Pathology and Laboratory Medicine, School of Medicine, the University of California Irvine, Irvine, CA, United States
| | - Mahmoud Singer
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Hawa Vahed
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Anthony B Nesburn
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Baruch D Kuppermann
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Jeffrey B Ulmer
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Daniel Gil
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Trevor M Jones
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Lbachir BenMohamed
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
- Division of Infectious Diseases and Hospitalist Program, Department of Medicine, School of Medicine, the University of California Irvine, Irvine, CA, United States
- Institute for Immunology; University of California Irvine, School of Medicine, Irvine, CA, United States
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5
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Aksu M, Kumar P, Güttler T, Taxer W, Gregor K, Mußil B, Rymarenko O, Stegmann KM, Dickmanns A, Gerber S, Reineking W, Schulz C, Henneck T, Mohamed A, Pohlmann G, Ramazanoglu M, Mese K, Groß U, Ben-Yedidia T, Ovadia O, Fischer DW, Kamensky M, Reichman A, Baumgärtner W, von Köckritz-Blickwede M, Dobbelstein M, Görlich D. Nanobodies to multiple spike variants and inhalation of nanobody-containing aerosols neutralize SARS-CoV-2 in cell culture and hamsters. Antiviral Res 2024; 221:105778. [PMID: 38065245 DOI: 10.1016/j.antiviral.2023.105778] [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: 08/25/2023] [Revised: 11/23/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
The ongoing threat of COVID-19 has highlighted the need for effective prophylaxis and convenient therapies, especially for outpatient settings. We have previously developed highly potent single-domain (VHH) antibodies, also known as nanobodies, that target the Receptor Binding Domain (RBD) of the SARS-CoV-2 Spike protein and neutralize the Wuhan strain of the virus. In this study, we present a new generation of anti-RBD nanobodies with superior properties. The primary representative of this group, Re32D03, neutralizes Alpha to Delta as well as Omicron BA.2.75; other members neutralize, in addition, Omicron BA.1, BA.2, BA.4/5, and XBB.1. Crystal structures of RBD-nanobody complexes reveal how ACE2-binding is blocked and also explain the nanobodies' tolerance to immune escape mutations. Through the cryo-EM structure of the Ma16B06-BA.1 Spike complex, we demonstrated how a single nanobody molecule can neutralize a trimeric spike. We also describe a method for large-scale production of these nanobodies in Pichia pastoris, and for formulating them into aerosols. Exposing hamsters to these aerosols, before or even 24 h after infection with SARS-CoV-2, significantly reduced virus load, weight loss and pathogenicity. These results show the potential of aerosolized nanobodies for prophylaxis and therapy of coronavirus infections.
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Affiliation(s)
- Metin Aksu
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany
| | - Priya Kumar
- University Medical Center Göttingen, Dept. of Molecular Oncology, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Thomas Güttler
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany; Octapharma Biopharmaceuticals GmbH, Im Neuenheimer Feld 590, 69120 Heidelberg, Germany
| | - Waltraud Taxer
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kathrin Gregor
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany
| | - Bianka Mußil
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany
| | - Oleh Rymarenko
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kim M Stegmann
- University Medical Center Göttingen, Dept. of Molecular Oncology, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Antje Dickmanns
- University Medical Center Göttingen, Dept. of Molecular Oncology, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Sabrina Gerber
- University Medical Center Göttingen, Dept. of Molecular Oncology, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Wencke Reineking
- Department of Pathology, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Claudia Schulz
- Research Center for Emerging Infections and Zoonosis (RIZ), University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Timo Henneck
- Research Center for Emerging Infections and Zoonosis (RIZ), University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany; Department of Biochemistry, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Ahmed Mohamed
- Research Center for Emerging Infections and Zoonosis (RIZ), University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany; Department of Biochemistry, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Gerhard Pohlmann
- Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, Nikolai-Fuchs Str. 1, 30625 Hannover, Germany
| | - Mehmet Ramazanoglu
- Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, Nikolai-Fuchs Str. 1, 30625 Hannover, Germany
| | - Kemal Mese
- University Medical Center Göttingen, Dept. of Medical Microbiology and Virology, Kreuzbergring 57, 37075 Göttingen, Germany
| | - Uwe Groß
- University Medical Center Göttingen, Dept. of Medical Microbiology and Virology, Kreuzbergring 57, 37075 Göttingen, Germany
| | - Tamar Ben-Yedidia
- Scinai Immunotherapeutics Ltd., Jerusalem BioPark, Hadassah Ein Kerem, Jerusalem, 9112001, Israel
| | - Oded Ovadia
- Scinai Immunotherapeutics Ltd., Jerusalem BioPark, Hadassah Ein Kerem, Jerusalem, 9112001, Israel
| | - Dalit Weinstein Fischer
- Scinai Immunotherapeutics Ltd., Jerusalem BioPark, Hadassah Ein Kerem, Jerusalem, 9112001, Israel
| | - Merav Kamensky
- Scinai Immunotherapeutics Ltd., Jerusalem BioPark, Hadassah Ein Kerem, Jerusalem, 9112001, Israel
| | - Amir Reichman
- Scinai Immunotherapeutics Ltd., Jerusalem BioPark, Hadassah Ein Kerem, Jerusalem, 9112001, Israel
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Maren von Köckritz-Blickwede
- Research Center for Emerging Infections and Zoonosis (RIZ), University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany; Department of Biochemistry, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Matthias Dobbelstein
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany; University Medical Center Göttingen, Dept. of Molecular Oncology, Justus von Liebig Weg 11, 37077 Göttingen, Germany.
| | - Dirk Görlich
- Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany.
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Zhang T, Zheng N, Wang Z, Xu X. Structure-based design of oligomeric receptor-binding domain (RBD) recombinant proteins as potent vaccine candidates against SARS-CoV-2. Hum Vaccin Immunother 2023; 19:2174755. [PMID: 36846890 PMCID: PMC10026890 DOI: 10.1080/21645515.2023.2174755] [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: 03/01/2023] Open
Abstract
The receptor-binding domain (RBD) of SARS-CoV-2 S protein is proved to be the major target of neutralizing antibodies. However, on the S protein, only a portion of epitopes in RBD can be effectively displayed with dynamic changes in spatial conformations. Using RBD fragment as antigen can better expose the neutralizing epitopes, but the immunogenicity of RBD monomer is suboptimal. Multimeric display of RBD molecules is a feasible strategy to optimize RBD-based vaccines. In this study, RBD single-chain dimer derived from Wuhan-Hu-1 was fused with a trimerization motif, and a cysteine was also introduced at the C-terminus. The resultant recombinant protein 2RBDpLC was expressed in Sf9 cells using a baculovirus expression system. Reducing/non-reducing PAGE, size-exclusion chromatography and in silico structure prediction indicated that 2RBDpLC polymerized and possibly formed RBD dodecamers through trimerization motif and intermolecular disulfide bonds. In mice, 2RBDpLC induced higher levels of RBD-specific and neutralizing antibody responses than RBD dimer, RBD trimer and prefusion-stabilized S protein (S2P). In addition, cross-neutralizing antibodies against Delta and Omicron VOC were also detected in the immune sera. Our results demonstrate that 2RBDpLC is a promising vaccine candidate, and the method of constructing dodecamers may be an effective strategy for designing RBD-based vaccines.
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Affiliation(s)
- Ting Zhang
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Ningchen Zheng
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Zhirong Wang
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Xuemei Xu
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
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7
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Mykytyn AZ, Fouchier RA, Haagmans BL. Antigenic evolution of SARS coronavirus 2. Curr Opin Virol 2023; 62:101349. [PMID: 37647851 DOI: 10.1016/j.coviro.2023.101349] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 09/01/2023]
Abstract
SARS coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, emerged in China in December 2019. Vaccines developed were very effective initially, however, the virus has shown remarkable evolution with multiple variants spreading globally over the last three years. Nowadays, newly emerging Omicron lineages are gaining substitutions at a fast rate, resulting in escape from neutralization by antibodies that target the Spike protein. Tools to map the impact of substitutions on the further antigenic evolution of SARS-CoV-2, such as antigenic cartography, may be helpful to update SARS-CoV-2 vaccines. In this review, we focus on the antigenic evolution of SARS-CoV-2, highlighting the impact of Spike protein substitutions individually and in combination on immune escape.
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Affiliation(s)
- Anna Z Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Ron Am Fouchier
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Bart L Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands.
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8
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Ratswohl C, Vázquez García C, Ahmad AUW, Gonschior H, Lebedin M, Silvis CE, Spatt L, Gerhard C, Lehmann M, Sander LE, Kurth F, Olsson S, de la Rosa K. A design strategy to generate a SARS-CoV-2 RBD vaccine that abrogates ACE2 binding and improves neutralizing antibody responses. Eur J Immunol 2023; 53:e2350408. [PMID: 37435628 DOI: 10.1002/eji.202350408] [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: 01/27/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/13/2023]
Abstract
The structure-based design of antigens holds promise for developing vaccines with higher efficacy and improved safety profiles. We postulate that abrogation of host receptor interaction bears potential for the improvement of vaccines by preventing antigen-induced modification of receptor function as well as the displacement or masking of the immunogen. Antigen modifications may yet destroy epitopes crucial for antibody neutralization. Here, we present a methodology that integrates deep mutational scans to identify and score SARS-CoV-2 receptor binding domain variants that maintain immunogenicity, but lack interaction with the widely expressed host receptor. Single point mutations were scored in silico, validated in vitro, and applied in vivo. Our top-scoring variant receptor binding domain-G502E prevented spike-induced cell-to-cell fusion, receptor internalization, and improved neutralizing antibody responses by 3.3-fold in rabbit immunizations. We name our strategy BIBAX for body-inert, B-cell-activating vaccines, which in the future may be applied beyond SARS-CoV-2 for the improvement of vaccines by design.
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Affiliation(s)
- Christoph Ratswohl
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Free University of Berlin, Berlin, Germany
| | - Clara Vázquez García
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité - Universitätsmedizin, Berlin, Germany
| | - Ata Ul Wakeel Ahmad
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité - Universitätsmedizin, Berlin, Germany
| | - Hannes Gonschior
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Mikhail Lebedin
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité - Universitätsmedizin, Berlin, Germany
| | - Casper Ewijn Silvis
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité - Universitätsmedizin, Berlin, Germany
| | - Lisa Spatt
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Cathrin Gerhard
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Leif E Sander
- Charité - Universitätsmedizin, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité, Berlin, Germany
| | | | - Simon Olsson
- Department of Computer Science and Engineering, Chalmers University of Technology, Göteborg, Västra Götalands län, Sweden
| | - Kathrin de la Rosa
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Berlin Institute of Health (BIH) at Charité, Berlin, Germany
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9
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Ma Q, Li M, Ma L, Zhang C, Zhang H, Zhong H, Wen J, Wang Y, Yan Z, Xiong W, Wu L, Guo J, Yang W, Yang Z, Zhang B. SARS-CoV-2 bivalent mRNA vaccine with broad protection against variants of concern. Front Immunol 2023; 14:1195299. [PMID: 37292197 PMCID: PMC10244545 DOI: 10.3389/fimmu.2023.1195299] [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: 03/28/2023] [Accepted: 05/04/2023] [Indexed: 06/10/2023] Open
Abstract
Introduction The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has rapidly spread around the globe. With a substantial number of mutations in its Spike protein, the SARS-CoV-2 Omicron variant is prone to immune evasion and led to the reduced efficacy of approved vaccines. Thus, emerging variants have brought new challenges to the prevention of COVID-19 and updated vaccines are urgently needed to provide better protection against the Omicron variant or other highly mutated variants. Materials and methods Here, we developed a novel bivalent mRNA vaccine, RBMRNA-405, comprising a 1:1 mix of mRNAs encoding both Delta-derived and Omicron-derived Spike proteins. We evaluated the immunogenicity of RBMRNA-405 in BALB/c mice and compared the antibody response and prophylactic efficacy induced by monovalent Delta or Omicron-specific vaccine with the bivalent RBMRNA-405 vaccine in the SARSCoV-2 variant challenge. Results Results showed that the RBMRNA-405 vaccine could generate broader neutralizing antibody responses against both Wuhan-Hu-1 and other SARS-CoV-2 variants, including Delta, Omicron, Alpha, Beta, and Gamma. RBMRNA-405 efficiently blocked infectious viral replication and lung injury in both Omicron- and Delta-challenged K18-ACE2 mice. Conclusion Our data suggest that RBMRNA-405 is a promising bivalent SARS-CoV-2 vaccine with broad-spectrum efficacy for further clinical development.
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Affiliation(s)
- Qinhai Ma
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Man Li
- Department of Drug Discovery and Development, Argorna Pharmaceuticals Co., Ltd, Guangzhou, China
| | - Lin Ma
- Department of Manufacturing, Guangzhou RiboBio Co., Ltd, Guangzhou, China
| | - Caroline Zhang
- Department of Manufacturing, Guangzhou RiboBio Co., Ltd, Guangzhou, China
| | - Hong Zhang
- Department of Drug Discovery and Development, Argorna Pharmaceuticals Co., Ltd, Guangzhou, China
| | - Huiling Zhong
- Department of Drug Discovery and Development, Argorna Pharmaceuticals Co., Ltd, Guangzhou, China
| | - Jian Wen
- Department of Manufacturing, Guangzhou RiboBio Co., Ltd, Guangzhou, China
| | - Yongsheng Wang
- Department of Drug Discovery and Development, Argorna Pharmaceuticals Co., Ltd, Guangzhou, China
| | - Zewei Yan
- Department of Drug Discovery and Development, Argorna Pharmaceuticals Co., Ltd, Guangzhou, China
| | - Wei Xiong
- Department of Manufacturing, Guangzhou RiboBio Co., Ltd, Guangzhou, China
| | - Linping Wu
- Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jianmin Guo
- Guangdong Provincial Key Laboratory of Drug Non-clinical Evaluation and Research, Guangdong Lewwin Pharmaceutical Research Institute Co., Ltd., Guangzhou, China
| | - Wei Yang
- Guangdong Provincial Key Laboratory of Drug Non-clinical Evaluation and Research, Guangdong Lewwin Pharmaceutical Research Institute Co., Ltd., Guangzhou, China
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, Macau SAR, China
| | - Biliang Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Drug Discovery and Development, Argorna Pharmaceuticals Co., Ltd, Guangzhou, China
- Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
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10
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Dangi T, Sanchez S, Lew MH, Awakoaiye B, Visvabharathy L, Richner JM, Koralnik IJ, Penaloza-MacMaster P. Pre-existing immunity modulates responses to mRNA boosters. Cell Rep 2023; 42:112167. [PMID: 36857186 PMCID: PMC9928730 DOI: 10.1016/j.celrep.2023.112167] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/19/2022] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
mRNA vaccines are effective in preventing severe COVID-19, but breakthrough infections, emerging variants, and waning immunity warrant the use of boosters. Although mRNA boosters are being implemented, the extent to which pre-existing immunity influences the efficacy of boosters remains unclear. In a cohort of individuals primed with the mRNA-1273 or BNT162b2 vaccines, we report that lower antibody levels before boost are associated with higher fold-increase in antibody levels after boost, suggesting that pre-existing antibody modulates the immunogenicity of mRNA vaccines. Our studies in mice show that pre-existing antibodies accelerate the clearance of vaccine antigen via Fc-dependent mechanisms, limiting the amount of antigen available to prime B cell responses after mRNA boosters. These data demonstrate a "tug of war" between pre-existing antibody responses and de novo B cell responses following mRNA vaccination, and they suggest that transient downmodulation of antibody effector function may improve the efficacy of mRNA boosters.
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Affiliation(s)
- Tanushree Dangi
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Sarah Sanchez
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Min Han Lew
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Bakare Awakoaiye
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lavanya Visvabharathy
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Justin M Richner
- Department of Microbiology and Immunology, University of Illinois Chicago College of Medicine, Chicago, IL 60612, USA
| | - Igor J Koralnik
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Pablo Penaloza-MacMaster
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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11
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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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12
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Underwood AP, Sølund C, Fernandez-Antunez C, Villadsen SL, Mikkelsen LS, Fahnøe U, Bollerup S, Winckelmann AA, Schneider UV, Binderup A, Vizgirda G, Sørensen AL, Vinten CN, Dalegaard MI, Ramirez S, Weis N, Bukh J. Durability and breadth of neutralisation following multiple antigen exposures to SARS-CoV-2 infection and/or COVID-19 vaccination. EBioMedicine 2023; 89:104475. [PMID: 36870117 PMCID: PMC9978324 DOI: 10.1016/j.ebiom.2023.104475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/28/2023] [Accepted: 01/31/2023] [Indexed: 03/06/2023] Open
Abstract
BACKGROUND Given the importance of vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the prevention of severe coronavirus disease 2019 (COVID-19), detailed long-term analyses of neutralising antibody responses are required to inform immunisation strategies. METHODS In this study, longitudinal neutralising antibody titres to an ancestral SARS-CoV-2 isolate and cross-neutralisation to delta and omicron isolates were analysed in individuals previously infected with SARS-CoV-2, vaccinated against COVID-19, or a complex mix thereof with up to two years of follow-up. FINDINGS Both infection-induced and vaccine-induced neutralising responses against SARS-CoV-2 appeared to follow similar decay patterns. Following vaccination in previously infected individuals, neutralising antibody responses were more durable than prior to vaccination. Further, this study shows that vaccination after infection, as well as booster vaccination, increases the cross-neutralising potential to both delta and omicron SARS-CoV-2 variants. INTERPRETATION Taken together, these results suggest that neither type of antigen exposure is superior for neutralising antibody durability. However, these results support vaccination to increase the durability and cross-neutralisation potential of neutralising responses, thereby enhancing protection against severe COVID-19. FUNDING This work was supported by grants from The Capital Region of Denmark's Research Foundation, the Novo Nordisk Foundation, the Independent Research Fund Denmark, the Candys Foundation, and the Danish Agency for Science and Higher Education.
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Affiliation(s)
- Alexander P Underwood
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Christina Sølund
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Carlota Fernandez-Antunez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Signe Lysemose Villadsen
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Lotte S Mikkelsen
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Ulrik Fahnøe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Signe Bollerup
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Anni Assing Winckelmann
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Uffe Vest Schneider
- Department of Clinical Microbiology, Copenhagen University Hospital, Hvidovre, Denmark
| | - Alekxander Binderup
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Greta Vizgirda
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Anna-Louise Sørensen
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | | | | | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Nina Weis
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark.
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13
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Das NC, Chakraborty P, Bayry J, Mukherjee S. Comparative Binding Ability of Human Monoclonal Antibodies against Omicron Variants of SARS-CoV-2: An In Silico Investigation. Antibodies (Basel) 2023; 12:antib12010017. [PMID: 36975364 PMCID: PMC10045060 DOI: 10.3390/antib12010017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/26/2023] Open
Abstract
Mutation(s) in the spike protein is the major characteristic trait of newly emerged SARS-CoV-2 variants such as Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Delta-plus. Omicron (B.1.1.529) is the latest addition and it has been characterized by high transmissibility and the ability to escape host immunity. Recently developed vaccines and repurposed drugs exert limited action on Omicron strains and hence new therapeutics are immediately needed. Herein, we have explored the efficiency of twelve therapeutic monoclonal antibodies (mAbs) targeting the RBD region of the spike glycoprotein against all the Omicron variants bearing a mutation in spike protein through molecular docking and molecular dynamics simulation. Our in silico evidence reveals that adintivimab, beludivimab, and regadanivimab are the most potent mAbs to form strong biophysical interactions and neutralize most of the Omicron variants. Considering the efficacy of mAbs, we incorporated CDRH3 of beludavimab within the framework of adintrevimab, which displayed a more intense binding affinity towards all of the Omicron variants viz. BA.1, BA.2, BA.2.12.1, BA.4, and BA.5. Furthermore, the cDNA of chimeric mAb was cloned in silico within pET30ax for recombinant production. In conclusion, the present study represents the candidature of human mAbs (beludavimab and adintrevimab) and the therapeutic potential of designed chimeric mAb for treating Omicron-infected patients.
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Affiliation(s)
- Nabarun Chandra Das
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol 713 340, India
| | - Pritha Chakraborty
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol 713 340, India
| | - Jagadeesh Bayry
- Department of Biological Sciences & Engineering, Indian Institute of Technology Palakkad, Palakkad 678 623, India
- Correspondence: (J.B.); or (S.M.)
| | - Suprabhat Mukherjee
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol 713 340, India
- Correspondence: (J.B.); or (S.M.)
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14
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Zhou SH, Zhang RY, You ZW, Zou YK, Wen Y, Wang J, Ding D, Bian MM, Zhang ZM, Yuan H, Yang GF, Guo J. pH-Sensitive and Biodegradable Mn 3(PO 4) 2·3H 2O Nanoparticles as an Adjuvant of Protein-Based Bivalent COVID-19 Vaccine to Induce Potent and Broad-Spectrum Immunity. ACS APPLIED MATERIALS & INTERFACES 2023; 15:acsami.2c19736. [PMID: 36748861 PMCID: PMC9924082 DOI: 10.1021/acsami.2c19736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Developing a novel and potent adjuvant with great biocompatibility for immune response augmentation is of great significance to enhance vaccine efficacy. In this work, we prepared a long-term stable, pH-sensitive, and biodegradable Mn3(PO4)2·3H2O nanoparticle (nano-MnP) by simply mixing MnCl2/NaH2PO4/Na2HPO4 solution for the first time and employed it as an immune stimulant in the bivalent COVID-19 protein vaccine comprised of wild-type S1 (S1-WT) and Omicron S1 (S1-Omicron) proteins as antigens to elicit a broad-spectrum immunity. The biological experiments indicated that the nano-MnP could effectively activate antigen-presenting cells through the cGAS-STING pathway. Compared with the conventional Alum-adjuvanted group, the nano-MnP-adjuvanted bivalent vaccine elicited approximately 7- and 8-fold increases in IgG antibody titers and antigen-specific IFN-γ secreting T cells, respectively. Importantly, antisera of the nano-MnP-adjuvanted group could effectively cross-neutralize the SARS-CoV-2 and its five variants of concern (VOCs) including Alpha, Beta, Gamma, Delta, and Omicron, demonstrating that this bivalent vaccine based on S1-WT and S1-Omicron proteins is an effective vaccine design strategy to induce broad-spectrum immune responses. Collectively, this nano-MnP material may provide a novel and efficient adjuvant platform for various prophylactic and therapeutic vaccines and provide insights for the development of the next-generation manganese adjuvant.
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Affiliation(s)
| | | | - Zi-Wei You
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education,
International Joint Research Center for Intelligent Biosensing Technology and Health,
Hubei International Scientific and Technological Cooperation Base of Pesticide and Green
Synthesis, College of Chemistry, Central China Normal
University, Wuhan 430079, China
| | - Yong-Ke Zou
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education,
International Joint Research Center for Intelligent Biosensing Technology and Health,
Hubei International Scientific and Technological Cooperation Base of Pesticide and Green
Synthesis, College of Chemistry, Central China Normal
University, Wuhan 430079, China
| | - Yu Wen
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education,
International Joint Research Center for Intelligent Biosensing Technology and Health,
Hubei International Scientific and Technological Cooperation Base of Pesticide and Green
Synthesis, College of Chemistry, Central China Normal
University, Wuhan 430079, China
| | - Jian Wang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education,
International Joint Research Center for Intelligent Biosensing Technology and Health,
Hubei International Scientific and Technological Cooperation Base of Pesticide and Green
Synthesis, College of Chemistry, Central China Normal
University, Wuhan 430079, China
| | - Dong Ding
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education,
International Joint Research Center for Intelligent Biosensing Technology and Health,
Hubei International Scientific and Technological Cooperation Base of Pesticide and Green
Synthesis, College of Chemistry, Central China Normal
University, Wuhan 430079, China
| | - Miao-Miao Bian
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education,
International Joint Research Center for Intelligent Biosensing Technology and Health,
Hubei International Scientific and Technological Cooperation Base of Pesticide and Green
Synthesis, College of Chemistry, Central China Normal
University, Wuhan 430079, China
| | - Zhi-Ming Zhang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education,
International Joint Research Center for Intelligent Biosensing Technology and Health,
Hubei International Scientific and Technological Cooperation Base of Pesticide and Green
Synthesis, College of Chemistry, Central China Normal
University, Wuhan 430079, China
| | - Hong Yuan
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education,
International Joint Research Center for Intelligent Biosensing Technology and Health,
Hubei International Scientific and Technological Cooperation Base of Pesticide and Green
Synthesis, College of Chemistry, Central China Normal
University, Wuhan 430079, China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education,
International Joint Research Center for Intelligent Biosensing Technology and Health,
Hubei International Scientific and Technological Cooperation Base of Pesticide and Green
Synthesis, College of Chemistry, Central China Normal
University, Wuhan 430079, China
| | - Jun Guo
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education,
International Joint Research Center for Intelligent Biosensing Technology and Health,
Hubei International Scientific and Technological Cooperation Base of Pesticide and Green
Synthesis, College of Chemistry, Central China Normal
University, Wuhan 430079, China
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15
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Mahalingam G, Periyasami Y, Arjunan P, Subaschandrabose RK, Mathivanan TV, Mathew RS, Devi RKT, Premkumar PS, Muliyil J, Srivastava A, Moorthy M, Marepally S. Omicron infection increases IgG binding to spike protein of predecessor variants. J Med Virol 2023; 95:e28419. [PMID: 36546401 PMCID: PMC9880675 DOI: 10.1002/jmv.28419] [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] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission in India in 2020-2022 was driven predominantly by Wild (Wuhan-Hu-1 and D614G), Delta, and Omicron variants. The aim of this study was to examine the effect of infections on the humoral immune response and cross-reactivity to spike proteins of Wuhan-Hu-1, Delta, C.1.2., and Omicron. Residual archival sera (N = 81) received between January 2020 and March 2022 were included. Infection status was inferred by a positive SARS-CoV-2 RT-PCR and/or serology (anti-N and anti-S antibodies) and sequencing of contemporaneous samples (N = 18) to infer lineage. We estimated the levels and cross-reactivity of infection-induced sera including Wild, Delta, Omicron as well as vaccine breakthrough infections (Delta and Omicron). We found an approximately two-fold increase in spike-specific IgG antibody binding in post-Omicron infection compared with the pre-Omicron period, whilst the change in pre- and post-Delta infections were similar. Further investigation of Omicron-specific humoral responses revealed primary Omicron infection as an inducer of cross-reactive antibodies against predecessor variants, in spite of the weaker degree of humoral response compared to Wuhan-Hu-1 and Delta infection. Intriguingly, Omicron vaccine-breakthrough infections when compared with primary infections, exhibited increased humoral responses against RBD (7.7-fold) and Trimeric S (Trimeric form of spike protein) (34.6-fold) in addition to increased binding of IgGs towards previously circulating variants (4.2 - 6.5-fold). Despite Delta breakthrough infections showing a higher level of humoral response against RBD (2.9-fold) and Trimeric S (5.7-fold) compared to primary Delta sera, a demonstrably reduced binding (36%-49%) was observed to Omicron spike protein. Omicron vaccine breakthrough infection results in increased intensity of humoral response and wider breadth of IgG binding to spike proteins of antigenically-distinct, predecessor variants.
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Affiliation(s)
- Gokulnath Mahalingam
- Centre for Stem Cell Research (CSCR) (a unit of inStem, Bengaluru)Christian Medical CollegeVelloreTamil NaduIndia
| | - Yogapriya Periyasami
- Centre for Stem Cell Research (CSCR) (a unit of inStem, Bengaluru)Christian Medical CollegeVelloreTamil NaduIndia
| | - Porkizhi Arjunan
- Centre for Stem Cell Research (CSCR) (a unit of inStem, Bengaluru)Christian Medical CollegeVelloreTamil NaduIndia
| | | | - Tamil V. Mathivanan
- Department of Clinical VirologyChristian Medical CollegeVelloreTamil NaduIndia
| | - Roshlin S. Mathew
- Department of Clinical VirologyChristian Medical CollegeVelloreTamil NaduIndia
| | - Ramya K. T. Devi
- Department of BiotechnologySRM Institute of Science and TechnologyTamil NaduIndia
| | | | | | - Alok Srivastava
- Centre for Stem Cell Research (CSCR) (a unit of inStem, Bengaluru)Christian Medical CollegeVelloreTamil NaduIndia
| | - Mahesh Moorthy
- Department of Clinical VirologyChristian Medical CollegeVelloreTamil NaduIndia
| | - Srujan Marepally
- Centre for Stem Cell Research (CSCR) (a unit of inStem, Bengaluru)Christian Medical CollegeVelloreTamil NaduIndia
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16
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Lei Z, Zhu L, Pan P, Ruan Z, Gu Y, Xia X, Wang S, Ge W, Yao Y, Luo F, Xiao H, Guo J, Ding Q, Yin Z, Li Y, Luo Z, Zhang Q, Chen X, Wu J. A vaccine delivery system promotes strong immune responses against SARS-CoV-2 variants. J Med Virol 2023; 95:e28475. [PMID: 36606607 DOI: 10.1002/jmv.28475] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/29/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
Global coronavirus disease 2019 (COVID-19) pandemics highlight the need of developing vaccines with universal and durable protection against emerging SARS-CoV-2 variants. Here we developed an extended-release vaccine delivery system (GP-diABZI-RBD), consisting the original SARS-CoV-2 WA1 strain receptor-binding domain (RBD) as the antigen and diABZI stimulator of interferon genes (STING) agonist in conjunction with yeast β-glucan particles (GP-diABZI) as the platform. GP-diABZI-RBD could activate STING pathway and inhibit SARS-CoV-2 replication. Compared to diABZI-RBD, intraperitoneal injection of GP-diABZI-RBD elicited robust cellular and humoral immune responses in mice. Using SARS-CoV-2 GFP/ΔN transcription and replication-competent virus-like particle system (trVLP), we demonstrated that GP-diABZI-RBD-prototype vaccine exhibited the strongest and durable humoral immune responses and antiviral protection; whereas GP-diABZI-RBD-Omicron displayed minimum neutralization responses against trVLP. By using pseudotype virus (PsVs) neutralization assay, we found that GP-diABZI-RBD-Prototype, GP-diABZI-RBD-Delta, and GP-diABZI-RBD-Gamma immunized mice sera could efficiently neutralize Delta and Gamma PsVs, but had weak protection against Omicron PsVs. In contrast, GP-diABZI-RBD-Omicron immunized mice sera displayed the strongest neutralization response to Omicron PsVs. Taken together, the results suggest that GP-diABZI can serve as a promising vaccine delivery system for enhancing durable humoral and cellular immunity against broad SARS-CoV-2 variants. Our study provides important scientific basis for developing SARS-CoV-2 VOC-specific vaccines.
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Affiliation(s)
- Zhiwei Lei
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Leqing Zhu
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, China.,Guangzhou Laboratory, Bioland, Guangzhou, China
| | - Pan Pan
- Department of Cardiology, The First Affiliated Hospital of Jinan University, Guangzhou, China.,Foshan Institute of Medical Microbiology, Foshan, China
| | - Zhihui Ruan
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China.,Foshan Institute of Medical Microbiology, Foshan, China
| | - Yu Gu
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Xichun Xia
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, China
| | - Shengli Wang
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, China
| | - Weiwei Ge
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yangrong Yao
- Foshan Institute of Medical Microbiology, Foshan, China
| | - Fazeng Luo
- Foshan Institute of Medical Microbiology, Foshan, China
| | - Heng Xiao
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China.,Foshan Institute of Medical Microbiology, Foshan, China
| | - Jun Guo
- Department of Cardiology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Qiang Ding
- School of Medicine, Tsinghua University, Beijing, China
| | - Zhinan Yin
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, China
| | - Yongkui Li
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China.,Foshan Institute of Medical Microbiology, Foshan, China
| | - Zhen Luo
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China.,Foshan Institute of Medical Microbiology, Foshan, China
| | - Qiwei Zhang
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China.,Foshan Institute of Medical Microbiology, Foshan, China
| | - Xin Chen
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Jianguo Wu
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China.,Department of Cardiology, The First Affiliated Hospital of Jinan University, Guangzhou, China.,Foshan Institute of Medical Microbiology, Foshan, China.,State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
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17
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Gong X, Khan A, Wani MY, Ahmad A, Duse A. COVID-19: A state of art on immunological responses, mutations, and treatment modalities in riposte. J Infect Public Health 2023; 16:233-249. [PMID: 36603376 PMCID: PMC9798670 DOI: 10.1016/j.jiph.2022.12.019] [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: 09/07/2022] [Revised: 12/25/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
Over the last few years, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) unleashed a global public health catastrophe that had a substantial influence on human physical and mental health, the global economy, and socio-political dynamics. SARS-CoV-2 is a respiratory pathogen and the cause of ongoing COVID-19 pandemic, which testified how unprepared humans are for pandemics. Scientists and policymakers continue to face challenges in developing ideal therapeutic agents and vaccines, while at the same time deciphering the pathology and immunology of SARS-CoV-2. Challenges in the early part of the pandemic included the rapid development of diagnostic assays, vaccines, and therapeutic agents. The ongoing transmission of COVID-19 is coupled with the emergence of viral variants that differ in their transmission efficiency, virulence, and vaccine susceptibility, thus complicating the spread of the pandemic. Our understanding of how the human immune system responds to these viruses as well as the patient groups (such as the elderly and immunocompromised individuals) who are often more susceptible to serious illness have both been aided by this epidemic. COVID-19 causes different symptoms to occur at different stages of infection, making it difficult to determine distinct treatment regimens employed for the various clinical phases of the disease. Unsurprisingly, determining the efficacy of currently available medications and developing novel therapeutic strategies have been a process of trial and error. The global scientific community collaborated to research and develop vaccines at a neck-breaking speed. This review summarises the overall picture of the COVID-19 pandemic, different mutations in SARS-CoV-2, immune response, and the treatment modalities against SARS-CoV-2.
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Affiliation(s)
- Xiaolong Gong
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Amber Khan
- Department of Clinical Haematology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mohmmad Younus Wani
- Department of Chemistry, College of Science, University of Jeddah, P.O. Box 80327, Jeddah 21589, Kingdom of Saudi Arabia
| | - Aijaz Ahmad
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,Division of Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg, South Africa,Corresponding author at: Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Adriano Duse
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,Division of Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg, South Africa
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18
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Majed SO, Mustafa SA, Jalal PJ, Fatah MH, Miasko M, Jawhar Z, Karim AY. SARS-CoV-2 Omicron Variant Genomic and Phylogenetic Analysis in Iraqi Kurdistan Region. Genes (Basel) 2023; 14:173. [PMID: 36672914 PMCID: PMC9859166 DOI: 10.3390/genes14010173] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/31/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
Omicron variants have been classified as Variants of Concern (VOC) by the World Health Organization (WHO) ever since they first emerged as a result of a significant mutation in this variant, which showed to have an impact on transmissibility and virulence of the virus, as evidenced by the ongoing modifications in the SARS-CoV-2 virus. As a global pandemic, the Omicron variant also spread among the Kurdish population. This study aimed to analyze different strains from different cities of the Kurdistan region of Iraq to show the risk of infection and the impact of the various mutations on immune responses and vaccination. A total of 175 nasopharyngeal/oropharyngeal specimens were collected at West Erbil Emergency Hospital and confirmed for SARS-CoV-2 infection by RT-PCR. The genomes of the samples were sequenced using the Illumina COVID-Seq Method. The genome analysis was established based on previously published data in the GISAID database and compared to previously detected mutations in the Omicron variants, and that they belong to the BA.1 lineage and include most variations determined in other studies related to transmissibility, high infectivity and immune escape. Most of the mutations were found in the RBD (receptor binding domain), the region related to the escape from humoral immunity. Remarkably, these point mutations (G339D, S371L, S373P, S375F, T547K, D614G, H655Y, N679K and N969K) were also determined in this study, which were unique, and their impact should be addressed more. Overall, the Omicron variants were more contagious than other variants. However, the mortality rate was low, and most infectious cases were asymptomatic. The next step should address the potential of Omicron variants to develop the next-generation COVID-19 vaccine.
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Affiliation(s)
- Sevan Omer Majed
- Biology Department, College of Education, Salahaddin University-Erbil, Erbil 44001, Kurdistan Region, Iraq
| | - Suhad Asad Mustafa
- General Directorate of Scientific Research Center, Salahaddin University-Erbil, Erbil 44001, Kurdistan Region, Iraq
| | - Paywast Jamal Jalal
- Biology Department, College of Science, University of Sulaimani, Sulaymaniyah 46001, Kurdistan Region, Iraq
| | - Mohammed Hassan Fatah
- Medical Lab., Technology Department, Kalar Technical College, Sulaimani Polytechnic University, Kalar 46021, Kurdistan Region, Iraq
| | - Monika Miasko
- Medical Analysis Department, Faculty of Applied Science, Tishk International University, Erbil 44001, Kurdistan Region, Iraq
| | - Zanko Jawhar
- Medical Laboratory Science, College of Health Sciences, Lebanese French University, Erbil 44001, Kurdistan Region, Iraq
| | - Abdulkarim Yasin Karim
- Department of Biology, College of Science, Salahaddin University-Erbil, Erbil 44001, Kurdistan Region, Iraq
- Department of Medical Microbiology, College of Science, Cihan University, Erbil 44001,Kurdistan Region, Iraq
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19
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Migueres M, Chapuy‐Regaud S, Miédougé M, Jamme T, Lougarre C, Da Silva I, Pucelle M, Staes L, Porcheron M, Diméglio C, Izopet J. Current immunoassays and detection of antibodies elicited by Omicron SARS-CoV-2 infection. J Med Virol 2023; 95:e28200. [PMID: 36207814 PMCID: PMC9874650 DOI: 10.1002/jmv.28200] [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: 07/14/2022] [Revised: 09/12/2022] [Accepted: 10/03/2022] [Indexed: 01/27/2023]
Abstract
The present study aimed to determine whether current commercial immunoassays are adequate for detecting anti-Omicron antibodies. We analyzed the anti-SARS-CoV-2 antibody response of 23 unvaccinated individuals 1-2 months after an Omicron infection. All blood samples were tested with a live virus neutralization assay using a clinical Omicron BA.1 strain and four commercial SARS-CoV-2 immunoassays. We assessed three anti-Spike immunoassays (SARS-CoV-2 IgG II Quant [Abbott S], Wantaï anti-SARS-CoV-2 antibody ELISA [Wantaï], Elecsys Anti-SARS-CoV-2 S assay [Roche]) and one anti-Nucleocapsid immunoassay (Abbott SARS-CoV-2 IgG assay [Abbott N]). Omicron neutralizing antibodies were detected in all samples with the live virus neutralization assay. The detection rate of the Abbott S, Wantai, Roche, and Abbott N immunoassays were 65.2%, 69.6%, 86.9%, and 91.3%, respectively. The sensitivities of Abbott S and Wantai immunoassays were significantly lower than that of the live virus neutralization assay (p = 0.004, p = 0.009; Fisher's exact test). Antibody concentrations obtained with anti-S immunoassays were correlated with Omicron neutralizing antibody concentrations. These data provide clinical evidence of the loss of performance of some commercial immunoassays to detect antibodies elicited by Omicron infections. It highlights the need to optimize these assays by adapting antigens to the circulating SARS-CoV-2 strains.
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Affiliation(s)
- Marion Migueres
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity) INSERM UMR1291 ‐ CNRS UMR5051ToulouseFrance,Université Toulouse III Paul‐SabatierToulouseFrance
| | - Sabine Chapuy‐Regaud
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity) INSERM UMR1291 ‐ CNRS UMR5051ToulouseFrance,Université Toulouse III Paul‐SabatierToulouseFrance
| | - Marcel Miédougé
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance
| | - Thibaut Jamme
- Laboratoire de Biochimie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance
| | | | - Isabelle Da Silva
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance
| | - Mélanie Pucelle
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance
| | - Laetitia Staes
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance
| | - Marion Porcheron
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance
| | - Chloé Diméglio
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity) INSERM UMR1291 ‐ CNRS UMR5051ToulouseFrance,Université Toulouse III Paul‐SabatierToulouseFrance
| | - Jacques Izopet
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity) INSERM UMR1291 ‐ CNRS UMR5051ToulouseFrance,Université Toulouse III Paul‐SabatierToulouseFrance
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20
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Silva SJRD, Kohl A, Pena L, Pardee K. Recent insights into SARS-CoV-2 omicron variant. Rev Med Virol 2023; 33:e2373. [PMID: 35662313 PMCID: PMC9347414 DOI: 10.1002/rmv.2373] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 04/25/2022] [Accepted: 05/18/2022] [Indexed: 01/28/2023]
Abstract
The SARS-CoV-2 omicron variant (B.1.1.529) was first identified in Botswana and South Africa, and its emergence has been associated with a steep increase in the number of SARS-CoV-2 infections. The omicron variant has subsequently spread very rapidly across the world, resulting in the World Health Organization classification as a variant of concern on 26 November 2021. Since its emergence, great efforts have been made by research groups around the world that have rapidly responded to fill our gaps in knowledge for this novel variant. A growing body of data has demonstrated that the omicron variant shows high transmissibility, robust binding to human angiotensin-converting enzyme 2 receptor, attenuated viral replication, and causes less severe disease in COVID-19 patients. Further, the variant has high environmental stability, high resistance against most therapeutic antibodies, and partial escape neutralisation by antibodies from convalescent patients or vaccinated individuals. With the pandemic ongoing, there is a need for the distillation of literature from primary research into an accessible format for the community. In this review, we summarise the key discoveries related to the SARS-CoV-2 omicron variant, highlighting the gaps in knowledge that guide the field's ongoing and future work.
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Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada.,Department of Virology, Laboratory of Virology and Experimental Therapy (LAVITE), Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Lindomar Pena
- Department of Virology, Laboratory of Virology and Experimental Therapy (LAVITE), Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil
| | - Keith Pardee
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada.,Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, Canada
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21
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Jimenez Ruiz JA, Lopez Ramirez C, Lopez-Campos JL. Spike protein of SARS-CoV-2 Omicron variant: An in-silico study evaluating spike interactions and immune evasion. Front Public Health 2022; 10:1052241. [PMID: 36523581 PMCID: PMC9746896 DOI: 10.3389/fpubh.2022.1052241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022] Open
Abstract
Background The fundamentals of the infectivity and immune evasion of the SARS-CoV-2 Omicron variant are not yet fully understood. Here, we carried out an in-silico study analyzing the spike protein, the protein electrostatic potential, and the potential immune evasion. Methods The analysis was based on the structure of the spike protein from two SARS-CoV-2 variants, the original Wuhan and the Botswana (Omicron). The full-length genome sequences and protein sequences were obtained from databanks. The interaction of the spike proteins with the human Angiotensin Converting Enzyme 2 (ACE2) receptor was evaluated through the open-source software. The Immune Epitope Database was used to analyze the potential immune evasion of the viruses. Results Our data show that the Omicron spike protein resulted in 37 amino acid changes. The physicochemical properties of the spike had changed, and the electrostatic potentials differed between both variants. This resulted in a decrease in protein interactions, which does not establish a greater interaction with the ACE2 receptor. These changes compromise key receptor-binding motif residues in the SARS-CoV-2 spike protein that interact with neutralizing antibodies and ACE2. Conclusions These mutations appear to confer enhanced properties of infectivity. The Omicron variant appears to be more effective at evading immune responses.
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Affiliation(s)
- Jose A. Jimenez Ruiz
- Research Group on Electronic Technology and Industrial Computing (TIC-150) at the University of Seville, Seville, Spain
| | - Cecilia Lopez Ramirez
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose Luis Lopez-Campos
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
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22
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Paniskaki K, Konik MJ, Anft M, Meister TL, Marheinecke C, Pfaender S, Jäger J, Krawczyk A, Zettler M, Dolff S, Westhoff TH, Rohn H, Stervbo U, Witzke O, Babel N. Superior humoral immunity in vaccinated SARS-CoV-2 convalescence as compared to SARS-COV-2 infection or vaccination. Front Immunol 2022; 13:1031254. [PMID: 36389833 PMCID: PMC9659602 DOI: 10.3389/fimmu.2022.1031254] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/20/2022] [Indexed: 11/24/2023] Open
Abstract
Emerging variants of concern (VOC) raise obstacles in shaping vaccination strategies and ending the pandemic. Vaccinated SARS-CoV-2 convalescence shapes the current immune dynamics. We analyzed the SARS-CoV-2 VOC-specific cellular and humoral response of 57 adults: 42 convalescent mRNA vaccinated patients (C+V+), 8 uninfected mRNA vaccinated (C-V+) and 7 unvaccinated convalescent individuals (C+V-). While C+V+ demonstrated a superior humoral SARS-CoV-2 response against all analyzed VOC (alpha, delta, omicron) compared to C-V+ and C+V-, SARS-CoV-2 reactive CD4+ and CD8+ T cells, which can cross-recognize the alpha, delta and omicron VOC after infection and/or vaccination were observed in all there groups without significant differences between the groups. We observed a preserved cross-reactive C+V+ and C-V+ T cell memory. An inferior humoral response but preserved cross-reactive T cell memory in C+V- compared to C+V+ was observed, as well as an inferior humoral response but preserved cross-reactive T cell memory in C+V- compared to C-V+. Adaptive immunity generated after SARS-CoV-2 infection and vaccination leads to superior humoral immune response against VOC compared to isolated infection or vaccination. Despite the apparent loss of neutralization potential caused by viral evolution, a preserved SARS-CoV-2 reactive T cell response with a robust potential for cross-recognition of the alpha, delta and omicron VOC was detected in all studied cohorts. Our results may have implications on current vaccination strategies.
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Affiliation(s)
- Krystallenia Paniskaki
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Margarethe J Konik
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Moritz Anft
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Toni L Meister
- Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | - Corinna Marheinecke
- Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | - Stephanie Pfaender
- Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | - Jasmin Jäger
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Adalbert Krawczyk
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Markus Zettler
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Sebastian Dolff
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Timm H Westhoff
- Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany
| | - Hana Rohn
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Ulrik Stervbo
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Oliver Witzke
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Nina Babel
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany
- Berlin Institute of Health at Charité - University Clinic Berlin, BIH Center for Regenerative Therapies (BCRT) Berlin, Berlin, Germany
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23
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Tubiana J, Xiang Y, Fan L, Wolfson HJ, Chen K, Schneidman-Duhovny D, Shi Y. Reduced B cell antigenicity of Omicron lowers host serologic response. Cell Rep 2022; 41:111512. [PMID: 36223774 PMCID: PMC9515332 DOI: 10.1016/j.celrep.2022.111512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/10/2022] [Accepted: 09/26/2022] [Indexed: 11/25/2022] Open
Abstract
The SARS-CoV-2 Omicron variant evades most neutralizing vaccine-induced antibodies and is associated with lower antibody titers upon breakthrough infections than previous variants. However, the mechanism remains unclear. Here, we find using a geometric deep-learning model that Omicron's extensively mutated receptor binding site (RBS) features reduced antigenicity compared with previous variants. Mice immunization experiments with different recombinant receptor binding domain (RBD) variants confirm that the serological response to Omicron is drastically attenuated and less potent. Analyses of serum cross-reactivity and competitive ELISA reveal a reduction in antibody response across both variable and conserved RBD epitopes. Computational modeling confirms that the RBS has a potential for further antigenicity reduction while retaining efficient receptor binding. Finally, we find a similar trend of antigenicity reduction over decades for hCoV229E, a common cold coronavirus. Thus, our study explains the reduced antibody titers associated with Omicron infection and reveals a possible trajectory of future viral evolution.
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Affiliation(s)
- Jérôme Tubiana
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 6997801, Israel,School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Yufei Xiang
- Center for Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Li Fan
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Haim J. Wolfson
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Kong Chen
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel.
| | - Yi Shi
- Center for Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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24
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Forsyth CB, Zhang L, Bhushan A, Swanson B, Zhang L, Mamede JI, Voigt RM, Shaikh M, Engen PA, Keshavarzian A. The SARS-CoV-2 S1 Spike Protein Promotes MAPK and NF-kB Activation in Human Lung Cells and Inflammatory Cytokine Production in Human Lung and Intestinal Epithelial Cells. Microorganisms 2022; 10:microorganisms10101996. [PMID: 36296272 PMCID: PMC9607240 DOI: 10.3390/microorganisms10101996] [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: 05/26/2022] [Revised: 09/12/2022] [Accepted: 10/05/2022] [Indexed: 11/18/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic began in January 2020 in Wuhan, China, with a new coronavirus designated SARS-CoV-2. The principal cause of death from COVID-19 disease quickly emerged as acute respiratory distress syndrome (ARDS). A key ARDS pathogenic mechanism is the “Cytokine Storm”, which is a dramatic increase in inflammatory cytokines in the blood. In the last two years of the pandemic, a new pathology has emerged in some COVID-19 survivors, in which a variety of long-term symptoms occur, a condition called post-acute sequelae of COVID-19 (PASC) or “Long COVID”. Therefore, there is an urgent need to better understand the mechanisms of the virus. The spike protein on the surface of the virus is composed of joined S1–S2 subunits. Upon S1 binding to the ACE2 receptor on human cells, the S1 subunit is cleaved and the S2 subunit mediates the entry of the virus. The S1 protein is then released into the blood, which might be one of the pivotal triggers for the initiation and/or perpetuation of the cytokine storm. In this study, we tested the hypothesis that the S1 spike protein is sufficient to activate inflammatory signaling and cytokine production, independent of the virus. Our data support a possible role for the S1 spike protein in the activation of inflammatory signaling and cytokine production in human lung and intestinal epithelial cells in culture. These data support a potential role for the SARS-CoV-2 S1 spike protein in COVID-19 pathogenesis and PASC.
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Affiliation(s)
- Christopher B. Forsyth
- Department of Internal Medicine, Section of Gastroenterology, Rush Center for Integrated Microbiome and Chronobiology Research, Department of Anatomy and Cell Biology, Rush University Graduate College, Rush University Medical Center, Chicago, IL 60612, USA
| | - Lijuan Zhang
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL 60612, USA
| | - Abhinav Bhushan
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Barbara Swanson
- Department of Adult Health & Gerontological Nursing, Rush University Medical Center, Chicago, IL 60612, USA
| | - Li Zhang
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612, USA
| | - João I. Mamede
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612, USA
| | - Robin M. Voigt
- Department of Internal Medicine, Section of Gastroenterology, Rush Center for Integrated Microbiome and Chronobiology Research, Department of Anatomy and Cell Biology, Rush University Graduate College, Rush University Medical Center, Chicago, IL 60612, USA
| | - Maliha Shaikh
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL 60612, USA
| | - Phillip A. Engen
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL 60612, USA
| | - Ali Keshavarzian
- Department of Internal Medicine, Section of Gastroenterology, Rush Center for Integrated Microbiome and Chronobiology Research, Department of Anatomy and Cell Biology, Rush University Graduate College, Rush University Medical Center, Chicago, IL 60612, USA
- Correspondence:
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25
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Kong W, Zhong Q, Chen M, Yu P, Xu R, Zhang L, Lai C, Deng M, Zhou Q, Xiong S, Liang Y, Wan L, Lin M, Wang M, Mai W, Chen L, Lei Y, Qin N, Zhu J, Ruan J, Huang Q, Kang A, Wang J, Li W, Ji T. Ad5-nCoV booster and Omicron variant breakthrough infection following two doses of inactivated vaccine elicit comparable antibody levels against Omicron variants. J Med Virol 2022; 95:e28163. [PMID: 36127294 PMCID: PMC9538621 DOI: 10.1002/jmv.28163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/18/2022] [Accepted: 09/14/2022] [Indexed: 01/11/2023]
Abstract
Little information is available for antibody levels against SARS-CoV-2 variants of concern induced by Omicron breakthrough infection and a third booster with an inactivated vaccine (InV) or Ad5-nCoV in people with completion of two InV doses. Plasma was collected from InV pre-vaccinated Omicron-infected patients (OIPs), unvaccinated OIPs between 0 and 22 days, and healthy donors (HDs) 14 days or 6 months after the second doses of an InV and 14 days after a homogenous booster or heterologous booster of Ad5-nCoV. Anti-Wuhan-, Anti-Delta-, and Anti-Omicron-receptor binding domain (RBD)-IgG titers were detected using enzyme-linked immunosorbent assay. InV pre-vaccinated OIPs had higher anti-Wuhan-, anti-Delta-, and anti-Omicron-RBD-IgG titers compared to unvaccinated OIPs. Anti-Wuhan-RBD-IgG titers sharply increased in InV pre-vaccinated OIPs 0-5 days postinfection (DPI), while the geometric mean titers (GMTs) of anti-Delta- and anti-Omicron-RBD-IgG were 3.3-fold and 12.0-fold lower. Then, the GMT of anti-Delta- and anti-Omicron-RBD-IgG increased to 35 112 and 28 186 during 11-22 DPI, about 2.6-fold and 3.2-fold lower, respectively, than the anti-Wuhan-RBD-IgG titer. The anti-Wuhan-, anti-Delta-, and anti-Omicron-RBD-IgG titers declined over time in HDs after two doses of an InV, with 25.2-fold, 5.6-fold, and 4.5-fold declination, respectively, at 6 months relative to the titers at 14 days after the second vaccination. Anti-Wuhan-, anti-Delta-, and anti-Omicron-RBD-IgG titers elicited by a heterologous Ad5-nCoV booster were significantly higher than those elicited by an InV booster, comparable to those in InV pre-vaccinated OIPs. InV and Ad5-nCoV boosters could improve humoral immunity against Omicron variants. Of these, the Ad5-nCoV booster is a better alternative.
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Affiliation(s)
- Weiya Kong
- Clinical Laboratory Medicine DepartmentThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Qingyang Zhong
- Department of Infectious DiseaseDongguan Ninth People's HospitalDongguanChina
| | - Mingxiao Chen
- Clinical Laboratory Medicine DepartmentThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Pei Yu
- Clinical Laboratory Medicine DepartmentThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Ruhong Xu
- Department of RespiratoryDongguan Ninth People's HospitalDongguanChina
| | - Lei Zhang
- Department of Kidney TransplantThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Changchun Lai
- Clinical Laboratory Medicine DepartmentMaoming People's HospitalMaomingChina
| | - Min Deng
- Clinical Laboratory Medicine DepartmentThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Qiang Zhou
- Clinical Laboratory Medicine DepartmentThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Shilong Xiong
- Clinical Laboratory Medicine DepartmentThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Yuemei Liang
- Clinical Laboratory Medicine DepartmentDongguan Ninth People's HospitalDongguanChina
| | - Li Wan
- Clinical Laboratory Medicine DepartmentThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Meifang Lin
- Clinical Laboratory Medicine DepartmentThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Minhong Wang
- Clinical Laboratory Medicine DepartmentThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Weikang Mai
- Clinical Laboratory Medicine DepartmentThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Lu Chen
- Clinical Laboratory Medicine DepartmentThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Yu Lei
- Clinical Laboratory Medicine DepartmentThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Nan Qin
- Clinical Laboratory Medicine DepartmentThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Jianqiang Zhu
- Clinical Laboratory Medicine DepartmentThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Jianfeng Ruan
- Hospital Infection‐Control DepartmentThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Qiulan Huang
- Department of Medical ExaminationThe Second Affiliated Hospital of Guangzhou Medical UniversityChina
| | - An Kang
- Department of Medical ExaminationThe Second Affiliated Hospital of Guangzhou Medical UniversityChina
| | - Jun Wang
- Immunization Planning SectionHaizhu District Center for Disease Control and PreventionGuangzhouChina
| | - Wenrui Li
- Clinical Laboratory Medicine DepartmentDongguan Ninth People's HospitalDongguanChina
| | - Tianxing Ji
- Clinical Laboratory Medicine DepartmentThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
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26
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A self-assembled trimeric protein vaccine induces protective immunity against Omicron variant. Nat Commun 2022; 13:5459. [PMID: 36115859 PMCID: PMC9482656 DOI: 10.1038/s41467-022-33209-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 09/08/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractThe recently emerged Omicron (B.1.1.529) variant has rapidly surpassed Delta to become the predominant circulating SARS-CoV-2 variant, given the higher transmissibility rate and immune escape ability, resulting in breakthrough infections in vaccinated individuals. A new generation of SARS-CoV-2 vaccines targeting the Omicron variant are urgently needed. Here, we developed a subunit vaccine named RBD-HR/trimer by directly linking the sequence of RBD derived from the Delta variant (containing L452R and T478K) and HR1 and HR2 in SARS-CoV-2 S2 subunit in a tandem manner, which can self-assemble into a trimer. In multiple animal models, vaccination of RBD-HR/trimer formulated with MF59-like oil-in-water adjuvant elicited sustained humoral immune response with high levels of broad-spectrum neutralizing antibodies against Omicron variants, also inducing a strong T cell immune response in vivo. In addition, our RBD-HR/trimer vaccine showed a strong boosting effect against Omicron variants after two doses of mRNA vaccines, featuring its capacity to be used in a prime-boost regimen. In mice and non-human primates, RBD-HR/trimer vaccination could confer a complete protection against live virus challenge of Omicron and Delta variants. The results qualified RBD-HR/trimer vaccine as a promising next-generation vaccine candidate for prevention of SARS-CoV-2, which deserved further evaluation in clinical trials.
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27
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Avnat E, Shapira G, Gurwitz D, Shomron N. Elevated Expression of RGS2 May Underlie Reduced Olfaction in COVID-19 Patients. J Pers Med 2022; 12:jpm12091396. [PMID: 36143181 PMCID: PMC9504192 DOI: 10.3390/jpm12091396] [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: 08/01/2022] [Revised: 08/15/2022] [Accepted: 08/25/2022] [Indexed: 12/03/2022] Open
Abstract
Anosmia is common in COVID-19 patients, lasting for weeks or months following recovery. The biological mechanism underlying olfactory deficiency in COVID-19 does not involve direct damage to nasal olfactory neurons, which do not express the proteins required for SARS-CoV-2 infection. A recent study suggested that anosmia results from downregulation of olfactory receptors. We hypothesized that anosmia in COVID-19 may also reflect SARS-CoV-2 infection-driven elevated expression of regulator of G protein signaling 2 (RGS2), a key regulator of odorant receptors, thereby silencing their signaling. To test our hypothesis, we analyzed gene expression of nasopharyngeal swabs from SARS-CoV-2 positive patients and non-infected controls (two published RNA-sequencing datasets, 580 individuals). Our analysis found upregulated RGS2 expression in SARS-CoV-2 positive patients (FC = 14.5, Padj = 1.69 × 10−5 and FC = 2.4; Padj = 0.001, per dataset). Additionally, RGS2 expression was strongly correlated with PTGS2, IL1B, CXCL8, NAMPT and other inflammation markers with substantial upregulation in early infection. These observations suggest that upregulated expression of RGS2 may underlie anosmia in COVID-19 patients. As a regulator of numerous G-protein coupled receptors, RGS2 may drive further neurological symptoms of COVID-19. Studies are required for clarifying the cellular mechanisms by which SARS-CoV-2 infection drives the upregulation of RGS2 and other genes implicated in inflammation. Insights on these pathway(s) may assist in understanding anosmia and additional neurological symptoms reported in COVID-19 patients.
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Affiliation(s)
- Eden Avnat
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Guy Shapira
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - David Gurwitz
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
- Correspondence: (D.G.); (N.S.); Tel.: +972-3-640-7611 (D.G.); +972-3-640-6594 (N.S.)
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
- Correspondence: (D.G.); (N.S.); Tel.: +972-3-640-7611 (D.G.); +972-3-640-6594 (N.S.)
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28
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Musazadeh V, Karimi A, Bagheri N, Jafarzadeh J, Sanaei S, Vajdi M, Karimi M, Niazkar HR. The favorable impacts of silibinin polyphenols as adjunctive therapy in reducing the complications of COVID-19: A review of research evidence and underlying mechanisms. Biomed Pharmacother 2022; 154:113593. [PMID: 36027611 PMCID: PMC9393179 DOI: 10.1016/j.biopha.2022.113593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 11/11/2022] Open
Abstract
The proceeding pandemic of coronavirus disease 2019 is the latest global challenge. Like most other infectious diseases, inflammation, oxidative stress, and immune system dysfunctions play a pivotal role in the pathogenesis of COVID-19. Furthermore, the quest of finding a potential pharmaceutical therapy for preventing and treating COVID-19 is still ongoing. Silymarin, a mixture of flavonolignans extracted from the milk thistle, has exhibited numerous therapeutic benefits. We reviewed the beneficial effects of silymarin on oxidative stress, inflammation, and the immune system, as primary factors involved in the pathogenesis of COVID-19. We searched PubMed/Medline, Web of Science, Scopus, and Science Direct databases up to April 2022 using the relevant keywords. In summary, the current review indicates that silymarin might exert therapeutic effects against COVID-19 by improving the antioxidant system, attenuating inflammatory response and respiratory distress, and enhancing immune system function. Silymarin can also bind to target proteins of SARS-CoV-2, including main protease, spike glycoprotein, and RNA-dependent RNA-polymerase, leading to the inhibition of viral replication. Although multiple lines of evidence suggest the possible promising impacts of silymarin in COVID-19, further clinical trials are encouraged.
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Affiliation(s)
- Vali Musazadeh
- Nutrition Research Center, Department of Clinical Nutrition, School of Nutrition and Food Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Arash Karimi
- Nutrition Research Center, Department of Clinical Nutrition, School of Nutrition and Food Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Nasim Bagheri
- Department of microbiology Islamic Azad University of medical science, Tehran, Iran
| | - Jaber Jafarzadeh
- Nutrition Research Center, Department of Clinical Nutrition, School of Nutrition and Food Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sarvin Sanaei
- Research Center for Integrative Medicine in Aging, Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahdi Vajdi
- Student Research Committee, Department of Clinical Nutrition, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mozhde Karimi
- Department of Immunology, Faculty ofMedical Sciences ,Tarbiat Modares University
| | - Hamid Reza Niazkar
- Breast Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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29
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Mylonakis E, Lutaakome J, Jain MK, Rogers AJ, Moltó J, Benet S, Mourad A, Files DC, Mugerwa H, Kityo C, Kiweewa F, Nalubega MG, Kitonsa J, Nabenkema E, Murray DD, Braun D, Kamel D, Higgs ES, Hatlen TJ, Kan VL, Sanchez A, Tierney J, Denner E, Wentworth D, Babiker AG, Davey VJ, Gelijns AC, Matthews GV, Thompson BT, Lane HC, Neaton JD, Lundgren JD. Lessons from an international trial evaluating vaccination strategies for recovered inpatients with COVID-19 (VATICO). MED 2022; 3:531-537. [PMID: 35963234 PMCID: PMC9373164 DOI: 10.1016/j.medj.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/07/2022] [Accepted: 07/15/2022] [Indexed: 12/30/2022]
Abstract
The protection provided by natural versus hybrid immunity from COVID-19 is unclear. We reflect on the challenges from trying to conduct a randomized post-SARS-CoV-2 infection vaccination trial study with rapidly evolving scientific data, vaccination guidelines, varying international policies, difficulties with vaccine availability, vaccine hesitancy, and a constantly evolving virus.
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Affiliation(s)
- Eleftherios Mylonakis
- Division of Infectious Diseases, Rhode Island Hospital & The Miriam Hospital, Alpert Medical School of Brown University, Providence, RI, USA.
| | | | - Mamta K Jain
- U.T. Southwestern Medical Center and Parkland Health and Hospital Systems, Dallas, TX, USA
| | - Angela J Rogers
- Pulmonary, Allergy and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - José Moltó
- Lluita contra la Sida Foundation & Infectious Diseases Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain, Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Carlos III Health Institute, Madrid, Spain
| | - Susana Benet
- Lluita contra la Sida Foundation & Infectious Diseases Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Ahmad Mourad
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - D Clark Files
- Division of Pulmonary, Critical Care, Allergy and Immunology, Department of Medicine, Wake Forest Baptist Medical Center, Winston-Salem, NC
| | - Henry Mugerwa
- Joint Clinical Research Centre, Lubowa and Gulu Regional Referral Hospital, Gulu, Uganda
| | - Cissy Kityo
- Joint Clinical Research Centre, Lubowa, Uganda
| | - Francis Kiweewa
- Makerere University Lung Institute (MLI), Kampala, Uganda; Lira Regional Referral Hospital, Lira, Uganda
| | | | | | | | - Daniel D Murray
- CHIP Center of Excellence for Health, Immunity, and Infections and Department of Infectious Diseases, Rigshospitalet; Copenhagen, Denmark
| | - Dominique Braun
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and Institute of Medical Virology, University of Zurich, Zurich Switzerland University Hospital Zurich, Zurich, Switzerland
| | - Dena Kamel
- UT Southwestern Medical Center, Internal Medicine, Infectious Diseases, Dallas, TX, USA
| | - Elizabeth S Higgs
- National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Timothy J Hatlen
- Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Virginia L Kan
- Infectious Diseases Section, VA Medical Center, Washington, DC, USA
| | | | - John Tierney
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | | | | | - Abdel G Babiker
- The Medical Research Council Clinical Trials Unit at UCL, University College London, London, UK
| | - Victoria J Davey
- United States Department of Veterans Affairs; Washington, DC, USA
| | - Annetine C Gelijns
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gail V Matthews
- The Kirby Institute, University of New South Wales, Sydney, Australia
| | - B Taylor Thompson
- Division of Pulmonary and Critical Care, Department of Medicine, Massachusetts General Hospital and Harvard Medical School; Boston, Massachusetts, USA
| | - H Clifford Lane
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - James D Neaton
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jens D Lundgren
- CHIP Center of Excellence for Health, Immunity, and Infections and Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark
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30
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Immune Escape Associated with RBD Omicron Mutations and SARS-CoV-2 Evolution Dynamics. Viruses 2022; 14:v14081603. [PMID: 35893668 PMCID: PMC9394476 DOI: 10.3390/v14081603] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023] Open
Abstract
The evolution and the emergence of new mutations of viruses affect their transmissibility and/or pathogenicity features, depending on different evolutionary scenarios of virus adaptation to the host. A typical trade-off scenario of SARS-CoV-2 evolution has been proposed, which leads to the appearance of an Omicron strain with lowered lethality, yet enhanced transmissibility. This direction of evolution might be partly explained by virus adaptation to therapeutic agents and enhanced escape from vaccine-induced and natural immunity formed by other SARS-CoV-2 strains. Omicron’s high mutation rate in the Spike protein, as well as its previously described high genome mutation rate (Kandeel et al., 2021), revealed a gap between it and other SARS-CoV-2 strains, indicating the absence of a transitional evolutionary form to the Omicron strain. Therefore, Omicron has emerged as a new serotype divergent from the evolutionary lineage of other SARS-CoV-2 strains. Omicron is a rapidly evolving variant of high concern, whose new subvariants continue to manifest. Its further understanding and the further monitoring of key mutations that provide virus immune escape and/or high affinity towards the receptor could be useful for vaccine and therapeutic development in order to control the evolutionary direction of the COVID-19 pandemic.
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31
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Sun W, He L, Lou H, Fan W, Yang L, Cheng G, Liu W, Sun L. The Cross-Protective Immunity Landscape Among Different SARS-CoV-2 Variant RBDs. Front Immunol 2022; 13:898520. [PMID: 35757743 PMCID: PMC9226324 DOI: 10.3389/fimmu.2022.898520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
Despite the fact that SARS-CoV-2 vaccines have been available in most parts of the world, the epidemic status remains grim with new variants emerging and escaping the immune protection of existing vaccines. Therefore, the development of more effective antigens and evaluation of their cross-protective immunity against different SARS-CoV-2 variants are particularly urgent. In this study, we expressed the wild type (WT), Alpha, Beta, Delta, and Lambda RBD proteins to immunize mice and evaluated their cross-neutralizing activity against different pseudoviruses (WT, Alpha, Beta, Delta, Lambda, and Omicron). All monovalent and pentavalent RBD antigens induced high titers of IgG antibodies against different variant RBD antigens. In contrast, WT RBD antigen-induced antibodies showed a lower neutralizing activity against Beta, Delta, Lambda, and Omicron pseudoviruses compared to neutralization against itself. Interestingly, Beta RBD antigen and multivalent antigen induced broader cross-neutralization antibodies than other variant RBD antigens. These data provide a reference for vaccine strain selection and universal COVID-19 vaccine design to fight the constant emergence of new SARS-CoV-2 variants.
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Affiliation(s)
- Wenqiang Sun
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Shenzhen Bay Laboratory, Institute of Infectious Diseases, Shenzhen, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning, China
| | - Lihong He
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Huicong Lou
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning, China
| | - Wenhui Fan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Limin Yang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Gong Cheng
- Shenzhen Bay Laboratory, Institute of Infectious Diseases, Shenzhen, China.,Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Wenjun Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Shenzhen Bay Laboratory, Institute of Infectious Diseases, Shenzhen, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Lei Sun
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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32
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Dangi T, Sanchez S, Lew MH, Visvabharathy L, Richner J, Koralnik IJ, Penaloza-MacMaster P. Pre-existing immunity modulates responses to mRNA boosters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.06.27.497248. [PMID: 35794898 PMCID: PMC9258286 DOI: 10.1101/2022.06.27.497248] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
mRNA vaccines have shown high efficacy in preventing severe COVID-19, but breakthrough infections, emerging variants and waning antibody levels have warranted the use of boosters. Although mRNA boosters have been widely implemented, the extent to which pre-existing immunity influences the efficacy of boosters remains unclear. In a cohort of individuals primed with the mRNA-1273 or BNT162b2 vaccines, we observed that lower antibody levels before boost were associated with higher fold-increase in antibody levels after boost, suggesting that pre-existing antibody modulates the boosting capacity of mRNA vaccines. Mechanistic studies in mice show that pre-existing antibodies significantly limit antigen expression and priming of B cell responses after mRNA vaccination. Furthermore, we demonstrate that the relative superiority of an updated Omicron vaccine over the original vaccine is critically dependent on the serostatus of the host. These data demonstrate that pre-existing immunity dictates responses to mRNA vaccination, elucidating specific circumstances when updated SARS-CoV-2 vaccines confer superior protection to original vaccines.
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Affiliation(s)
- Tanushree Dangi
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Sarah Sanchez
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Min Han Lew
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lavanya Visvabharathy
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Justin Richner
- Department of Microbiology & Immunology, University of Illinois Chicago College of Medicine, Chicago, IL 60612
| | - Igor J. Koralnik
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Pablo Penaloza-MacMaster
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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Nan BG, Zhang S, Li YC, Kang XP, Chen YH, Li L, Jiang T, Li J. Convolutional Neural Networks Based on Sequential Spike Predict the High Human Adaptation of SARS-CoV-2 Omicron Variants. Viruses 2022; 14:v14051072. [PMID: 35632811 PMCID: PMC9147419 DOI: 10.3390/v14051072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/04/2022] Open
Abstract
The COVID-19 pandemic has frequently produced more highly transmissible SARS-CoV-2 variants, such as Omicron, which has produced sublineages. It is a challenge to tell apart high-risk Omicron sublineages and other lineages of SARS-CoV-2 variants. We aimed to build a fine-grained deep learning (DL) model to assess SARS-CoV-2 transmissibility, updating our former coarse-grained model, with the training/validating data of early-stage SARS-CoV-2 variants and based on sequential Spike samples. Sequential amino acid (AA) frequency was decomposed into serially and slidingly windowed fragments in Spike. Unsupervised machine learning approaches were performed to observe the distribution in sequential AA frequency and then a supervised Convolutional Neural Network (CNN) was built with three adaptation labels to predict the human adaptation of Omicron variants in sublineages. Results indicated clear inter-lineage separation and intra-lineage clustering for SARS-CoV-2 variants in the decomposed sequential AAs. Accurate classification by the predictor was validated for the variants with different adaptations. Higher adaptation for the BA.2 sublineage and middle-level adaptation for the BA.1/BA.1.1 sublineages were predicted for Omicron variants. Summarily, the Omicron BA.2 sublineage is more adaptive than BA.1/BA.1.1 and has spread more rapidly, particularly in Europe. The fine-grained adaptation DL model works well for the timely assessment of the transmissibility of SARS-CoV-2 variants, facilitating the control of emerging SARS-CoV-2 variants.
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Affiliation(s)
| | | | | | | | | | | | | | - Jing Li
- Correspondence: (T.J.); (J.L.)
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