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Li P, Faraone JN, Hsu CC, Chamblee M, Zheng YM, Carlin C, Bednash JS, Horowitz JC, Mallampalli RK, Saif LJ, Oltz EM, Jones D, Li J, Gumina RJ, Xu K, Liu SL. Characteristics of JN.1-derived SARS-CoV-2 subvariants SLip, FLiRT, and KP.2 in neutralization escape, infectivity and membrane fusion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.20.595020. [PMID: 38826376 PMCID: PMC11142104 DOI: 10.1101/2024.05.20.595020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
SARS-CoV-2 variants derived from the immune evasive JN.1 are on the rise worldwide. Here, we investigated JN.1-derived subvariants SLip, FLiRT, and KP.2 for their ability to be neutralized by antibodies in bivalent-vaccinated human sera, XBB.1.5 monovalent-vaccinated hamster sera, sera from people infected during the BA.2.86/JN.1 wave, and class III monoclonal antibody (Mab) S309. We found that compared to parental JN.1, SLip and KP.2, and especially FLiRT, exhibit increased resistance to COVID-19 bivalent-vaccinated human sera and BA.2.86/JN.1-wave convalescent sera. Interestingly, antibodies in XBB.1.5 monovalent vaccinated hamster sera robustly neutralized FLiRT and KP.2 but had reduced efficiency for SLip. These JN.1 subvariants were resistant to neutralization by Mab S309. In addition, we investigated aspects of spike protein biology including infectivity, cell-cell fusion and processing, and found that these subvariants, especially SLip, had a decreased infectivity and membrane fusion relative to JN.1, correlating with decreased spike processing. Homology modeling revealed that L455S and F456L mutations in SLip reduced local hydrophobicity in the spike and hence its binding to ACE2. In contrast, the additional R346T mutation in FLiRT and KP.2 strengthened conformational support of the receptor-binding motif, thus counteracting the effects of L455S and F456L. These three mutations, alongside D339H, which is present in all JN.1 sublineages, alter the epitopes targeted by therapeutic Mabs, including class I and class III S309, explaining their reduced sensitivity to neutralization by sera and S309. Together, our findings provide insight into neutralization resistance of newly emerged JN.1 subvariants and suggest that future vaccine formulations should consider JN.1 spike as immunogen, although the current XBB.1.5 monovalent vaccine could still offer adequate protection.
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Affiliation(s)
- Pei Li
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Julia N. Faraone
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Cheng Chih Hsu
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Michelle Chamblee
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Yi-Min Zheng
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Claire Carlin
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Joseph S. Bednash
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Jeffrey C. Horowitz
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Rama K. Mallampalli
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Linda J. Saif
- Center for Food Animal Health, Animal Sciences Department, OARDC, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA
- Veterinary Preventive Medicine Department, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Eugene M. Oltz
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center Arthur G James Cancer Hospital and Richard J Solove Research Institute, Columbus, Ohio, USA
| | - Daniel Jones
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Jianrong Li
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Richard J. Gumina
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Kai Xu
- Texas Therapeutic Institute, Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
- Lead contact
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Guo H, Ha S, Botten JW, Xu K, Zhang N, An Z, Strohl WR, Shiver JW, Fu TM. SARS-CoV-2 Omicron: Viral Evolution, Immune Evasion, and Alternative Durable Therapeutic Strategies. Viruses 2024; 16:697. [PMID: 38793580 PMCID: PMC11125895 DOI: 10.3390/v16050697] [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: 04/10/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Since the SARS-CoV-2 Omicron virus has gained dominance worldwide, its continual evolution with unpredictable mutations and patterns has revoked all authorized immunotherapeutics. Rapid viral evolution has also necessitated several rounds of vaccine updates in order to provide adequate immune protection. It remains imperative to understand how Omicron evolves into different subvariants and causes immune escape as this could help reevaluate the current intervention strategies mostly implemented in the clinics as emergency measures to counter the pandemic and, importantly, develop new solutions. Here, we provide a review focusing on the major events of Omicron viral evolution, including the features of spike mutation that lead to immune evasion against monoclonal antibody (mAb) therapy and vaccination, and suggest alternative durable options such as the ACE2-based experimental therapies superior to mAbs to address this unprecedented evolution of Omicron virus. In addition, this type of unique ACE2-based virus-trapping molecules can counter all zoonotic SARS coronaviruses, either from unknown animal hosts or from established wild-life reservoirs of SARS-CoV-2, and even seasonal alpha coronavirus NL63 that depends on human ACE2 for infection.
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Affiliation(s)
- Hailong Guo
- IGM Biosciences, Mountain View, CA 94043, USA
| | - Sha Ha
- IGM Biosciences, Mountain View, CA 94043, USA
| | - Jason W. Botten
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405, USA
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Kai Xu
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ningyan Zhang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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Qian J, Zhang S, Wang F, Li J, Zhang J. What makes SARS-CoV-2 unique? Focusing on the spike protein. Cell Biol Int 2024; 48:404-430. [PMID: 38263600 DOI: 10.1002/cbin.12130] [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: 10/09/2023] [Revised: 12/25/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024]
Abstract
Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) seriously threatens public health and safety. Genetic variants determine the expression of SARS-CoV-2 structural proteins, which are associated with enhanced transmissibility, enhanced virulence, and immune escape. Vaccination is encouraged as a public health intervention, and different types of vaccines are used worldwide. However, new variants continue to emerge, especially the Omicron complex, and the neutralizing antibody responses are diminished significantly. In this review, we outlined the uniqueness of SARS-CoV-2 from three perspectives. First, we described the detailed structure of the spike (S) protein, which is highly susceptible to mutations and contributes to the distinct infection cycle of the virus. Second, we systematically summarized the immunoglobulin G epitopes of SARS-CoV-2 and highlighted the central role of the nonconserved regions of the S protein in adaptive immune escape. Third, we provided an overview of the vaccines targeting the S protein and discussed the impact of the nonconserved regions on vaccine effectiveness. The characterization and identification of the structure and genomic organization of SARS-CoV-2 will help elucidate its mechanisms of viral mutation and infection and provide a basis for the selection of optimal treatments. The leaps in advancements regarding improved diagnosis, targeted vaccines and therapeutic remedies provide sound evidence showing that scientific understanding, research, and technology evolved at the pace of the pandemic.
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Affiliation(s)
- Jingbo Qian
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Shichang Zhang
- Department of Clinical Laboratory Medicine, Shenzhen Hospital of Southern Medical University, Shenzhen, China
| | - Fang Wang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiexin Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
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4
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Chen X, Wang M, Liu X, Zhang W, Yan H, Lan X, Xu Y, Tang S, Xie J. Clustering analysis for the evolutionary relationships of SARS-CoV-2 strains. Sci Rep 2024; 14:6428. [PMID: 38499639 PMCID: PMC10948388 DOI: 10.1038/s41598-024-57001-5] [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: 11/16/2023] [Accepted: 03/13/2024] [Indexed: 03/20/2024] Open
Abstract
To explore the differences and relationships between the available SARS-CoV-2 strains and predict the potential evolutionary direction of these strains, we employ the hierarchical clustering analysis to investigate the evolutionary relationships between the SARS-CoV-2 strains utilizing the genomic sequences collected in China till January 7, 2023. We encode the sequences of the existing SARS-CoV-2 strains into numerical data through k-mer algorithm, then propose four methods to select the representative sample from each type of strains to comprise the dataset for clustering analysis. Three hierarchical clustering algorithms named Ward-Euclidean, Ward-Jaccard, and Average-Euclidean are introduced through combing the Euclidean and Jaccard distance with the Ward and Average linkage clustering algorithms embedded in the OriginPro software. Experimental results reveal that BF.28, BE.1.1.1, BA.5.3, and BA.5.6.4 strains exhibit distinct characteristics which are not observed in other types of SARS-CoV-2 strains, suggesting their being the majority potential sources which the future SARS-CoV-2 strains' evolution from. Moreover, BA.2.75, CH.1.1, BA.2, BA.5.1.3, BF.7, and B.1.1.214 strains demonstrate enhanced abilities in terms of immune evasion, transmissibility, and pathogenicity. Hence, closely monitoring the evolutionary trends of these strains is crucial to mitigate their impact on public health and society as far as possible.
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Affiliation(s)
- Xiangzhong Chen
- School of Computer Science, Shaanxi Normal University, Xian, 710119, China
| | - Mingzhao Wang
- School of Computer Science, Shaanxi Normal University, Xian, 710119, China
| | - Xinglin Liu
- School of Computer Science, Shaanxi Normal University, Xian, 710119, China
| | - Wenjie Zhang
- School of Computer Science, Shaanxi Normal University, Xian, 710119, China
| | - Huan Yan
- School of Computer Science, Shaanxi Normal University, Xian, 710119, China
| | - Xiang Lan
- School of Computer Science, Shaanxi Normal University, Xian, 710119, China
| | - Yandi Xu
- School of Computer Science, Shaanxi Normal University, Xian, 710119, China
- College of Life Sciences, Shaanxi Normal University, Xian, 710119, China
| | - Sanyi Tang
- School of Mathematics and Statistics, Shaanxi Normal University, Xian, 710119, China.
| | - Juanying Xie
- School of Computer Science, Shaanxi Normal University, Xian, 710119, China.
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5
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Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. AlphaFold2-Enabled Atomistic Modeling of Structure, Conformational Ensembles, and Binding Energetics of the SARS-CoV-2 Omicron BA.2.86 Spike Protein with ACE2 Host Receptor and Antibodies: Compensatory Functional Effects of Binding Hotspots in Modulating Mechanisms of Receptor Binding and Immune Escape. J Chem Inf Model 2024; 64:1657-1681. [PMID: 38373700 DOI: 10.1021/acs.jcim.3c01857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
The latest wave of SARS-CoV-2 Omicron variants displayed a growth advantage and increased viral fitness through convergent evolution of functional hotspots that work synchronously to balance fitness requirements for productive receptor binding and efficient immune evasion. In this study, we combined AlphaFold2-based structural modeling approaches with atomistic simulations and mutational profiling of binding energetics and stability for prediction and comprehensive analysis of the structure, dynamics, and binding of the SARS-CoV-2 Omicron BA.2.86 spike variant with ACE2 host receptor and distinct classes of antibodies. We adapted several AlphaFold2 approaches to predict both the structure and conformational ensembles of the Omicron BA.2.86 spike protein in the complex with the host receptor. The results showed that the AlphaFold2-predicted structural ensemble of the BA.2.86 spike protein complex with ACE2 can accurately capture the main conformational states of the Omicron variant. Complementary to AlphaFold2 structural predictions, microsecond molecular dynamics simulations reveal the details of the conformational landscape and produced equilibrium ensembles of the BA.2.86 structures that are used to perform mutational scanning of spike residues and characterize structural stability and binding energy hotspots. The ensemble-based mutational profiling of the receptor binding domain residues in the BA.2 and BA.2.86 spike complexes with ACE2 revealed a group of conserved hydrophobic hotspots and critical variant-specific contributions of the BA.2.86 convergent mutational hotspots R403K, F486P, and R493Q. To examine the immune evasion properties of BA.2.86 in atomistic detail, we performed structure-based mutational profiling of the spike protein binding interfaces with distinct classes of antibodies that displayed significantly reduced neutralization against the BA.2.86 variant. The results revealed the molecular basis of compensatory functional effects of the binding hotspots, showing that BA.2.86 lineage may have evolved to outcompete other Omicron subvariants by improving immune evasion while preserving binding affinity with ACE2 via through a compensatory effect of R493Q and F486P convergent mutational hotspots. This study demonstrated that an integrative approach combining AlphaFold2 predictions with complementary atomistic molecular dynamics simulations and robust ensemble-based mutational profiling of spike residues can enable accurate and comprehensive characterization of structure, dynamics, and binding mechanisms of newly emerging Omicron variants.
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Affiliation(s)
- Nishank Raisinghani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States of America
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States of America
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States of America
| | - Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States of America
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States of America
| | - Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States of America
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States of America
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6
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Qu P, Xu K, Faraone JN, Goodarzi N, Zheng YM, Carlin C, Bednash JS, Horowitz JC, Mallampalli RK, Saif LJ, Oltz EM, Jones D, Gumina RJ, Liu SL. Immune evasion, infectivity, and fusogenicity of SARS-CoV-2 BA.2.86 and FLip variants. Cell 2024; 187:585-595.e6. [PMID: 38194968 PMCID: PMC10872432 DOI: 10.1016/j.cell.2023.12.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/11/2023] [Accepted: 12/18/2023] [Indexed: 01/11/2024]
Abstract
Evolution of SARS-CoV-2 requires the reassessment of current vaccine measures. Here, we characterized BA.2.86 and XBB-derived variant FLip by investigating their neutralization alongside D614G, BA.1, BA.2, BA.4/5, XBB.1.5, and EG.5.1 by sera from 3-dose-vaccinated and bivalent-vaccinated healthcare workers, XBB.1.5-wave-infected first responders, and monoclonal antibody (mAb) S309. We assessed the biology of the variant spikes by measuring viral infectivity and membrane fusogenicity. BA.2.86 is less immune evasive compared to FLip and other XBB variants, consistent with antigenic distances. Importantly, distinct from XBB variants, mAb S309 was unable to neutralize BA.2.86, likely due to a D339H mutation based on modeling. BA.2.86 had relatively high fusogenicity and infectivity in CaLu-3 cells but low fusion and infectivity in 293T-ACE2 cells compared to some XBB variants, suggesting a potentially different conformational stability of BA.2.86 spike. Overall, our study underscores the importance of SARS-CoV-2 variant surveillance and the need for updated COVID-19 vaccines.
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Affiliation(s)
- Panke Qu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Kai Xu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Julia N Faraone
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Negin Goodarzi
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Yi-Min Zheng
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Claire Carlin
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Joseph S Bednash
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Jeffrey C Horowitz
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Rama K Mallampalli
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Linda J Saif
- Center for Food Animal Health, Animal Sciences Department, OARDC, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; Veterinary Preventive Medicine Department, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA; Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Eugene M Oltz
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Daniel Jones
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Richard J Gumina
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA; Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA.
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7
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Zhang L, Kempf A, Nehlmeier I, Cossmann A, Richter A, Bdeir N, Graichen L, Moldenhauer AS, Dopfer-Jablonka A, Stankov MV, Simon-Loriere E, Schulz SR, Jäck HM, Čičin-Šain L, Behrens GMN, Drosten C, Hoffmann M, Pöhlmann S. SARS-CoV-2 BA.2.86 enters lung cells and evades neutralizing antibodies with high efficiency. Cell 2024; 187:596-608.e17. [PMID: 38194966 DOI: 10.1016/j.cell.2023.12.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/03/2023] [Accepted: 12/18/2023] [Indexed: 01/11/2024]
Abstract
BA.2.86, a recently identified descendant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2 sublineage, contains ∼35 mutations in the spike (S) protein and spreads in multiple countries. Here, we investigated whether the virus exhibits altered biological traits, focusing on S protein-driven viral entry. Employing pseudotyped particles, we show that BA.2.86, unlike other Omicron sublineages, enters Calu-3 lung cells with high efficiency and in a serine- but not cysteine-protease-dependent manner. Robust lung cell infection was confirmed with authentic BA.2.86, but the virus exhibited low specific infectivity. Further, BA.2.86 was highly resistant against all therapeutic antibodies tested, efficiently evading neutralization by antibodies induced by non-adapted vaccines. In contrast, BA.2.86 and the currently circulating EG.5.1 sublineage were appreciably neutralized by antibodies induced by the XBB.1.5-adapted vaccine. Collectively, BA.2.86 has regained a trait characteristic of early SARS-CoV-2 lineages, robust lung cell entry, and evades neutralizing antibodies. However, BA.2.86 exhibits low specific infectivity, which might limit transmissibility.
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Affiliation(s)
- Lu Zhang
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany
| | - Anne Cossmann
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Anja Richter
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Najat Bdeir
- Department of Viral Immunology, Helmholtz Zentrum für Infektionsforschung, 38124 Braunschweig, Germany
| | - Luise Graichen
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | | | - Alexandra Dopfer-Jablonka
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 30625 Hannover, Germany
| | - Metodi V Stankov
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Etienne Simon-Loriere
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, 75015 Paris, France; National Reference Center for Viruses of respiratory Infections, Institut Pasteur, 75015 Paris, France
| | - Sebastian R Schulz
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Luka Čičin-Šain
- Department of Viral Immunology, Helmholtz Zentrum für Infektionsforschung, 38124 Braunschweig, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 30625 Hannover, Germany; Center for Individualized Infection Medicine, a joint venture of HZI and MHH, 30625 Hannover, Germany
| | - Georg M N Behrens
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 30625 Hannover, Germany; Center for Individualized Infection Medicine, a joint venture of HZI and MHH, 30625 Hannover, Germany
| | - Christian Drosten
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany.
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany.
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8
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Yadav PD, Sardana V, Deshpande GR, Shinde PV, Thangaraj JWV, George LS, Sapkal GN, Patil DY, Sahay RR, Shete AM, Joshi M, Murhekar M, Godbole S, Gupta N, Prakash S, Rathore M, Ujjainiya R, Singh AP, Mishra A, Dash D, Chaudhary K, Sengupta S. Neutralizing antibody responses to SARS-CoV-2 Omicron variants: Post six months following two-dose & three-dose vaccination of ChAdOx1 nCoV-19 or BBV152. Indian J Med Res 2024; 159:223-231. [PMID: 38517215 PMCID: PMC11050759 DOI: 10.4103/ijmr.ijmr_948_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND OBJECTIVES The Omicron sub-lineages are known to have higher infectivity, immune escape and lower virulence. During December 2022 - January 2023 and March - April 2023, India witnessed increased SARS-CoV-2 infections, mostly due to newer Omicron sub-lineages. With this unprecedented rise in cases, we assessed the neutralization potential of individuals vaccinated with ChAdOx1 nCoV (Covishield) and BBV152 (Covaxin) against emerging Omicron sub-lineages. METHODS Neutralizing antibody responses were measured in the sera collected from individuals six months post-two doses (n=88) of Covishield (n=44) or Covaxin (n=44) and post-three doses (n=102) of Covishield (n=46) or Covaxin (n=56) booster dose against prototype B.1 strain, lineages of Omicron; XBB.1, BQ.1, BA.5.2 and BF.7. RESULTS The sera of individuals collected six months after the two-dose and the three-dose demonstrated neutralizing activity against all variants. The neutralizing antibody (NAbs) level was highest against the prototype B.1 strain, followed by BA5.2 (5-6 fold lower), BF.7 (11-12 fold lower), BQ.1 (12 fold lower) and XBB.1 (18-22 fold lower). INTERPRETATION CONCLUSIONS Persistence of NAb responses was comparable in individuals with two- and three-dose groups post six months of vaccination. Among the Omicron sub-variants, XBB.1 showed marked neutralization escape, thus pointing towards an eventual immune escape, which may cause more infections. Further, the correlation of study data with complete clinical profile of the participants along with observations for cell-mediated immunity may provide a clear picture for the sustained protection due to three-dose vaccination as well as hybrid immunity against the newer variants.
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Affiliation(s)
| | - Viren Sardana
- Big Data and Informatics Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | | | | | | | - Leyanna S. George
- Division of Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | | | | | - Rima R. Sahay
- Maximum Containment Laboratory, Pune, Maharashtra, India
| | - Anita M. Shete
- Maximum Containment Laboratory, Pune, Maharashtra, India
| | - Madhavi Joshi
- Department of Science & Technology, Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Manoj Murhekar
- Department of Epidemiology & Biostatistics, ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - Sheela Godbole
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Nivedita Gupta
- Division of Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Satyartha Prakash
- Big Data and Informatics Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Mamta Rathore
- Cardiometabolic Disease Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Rajat Ujjainiya
- Cardiometabolic Disease Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Ajay Pratap Singh
- Cardiometabolic Disease Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Aastha Mishra
- Cardiometabolic Disease Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Debasis Dash
- Cardiometabolic Disease Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Kumardeep Chaudhary
- Big Data and Informatics Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Shantanu Sengupta
- Big Data and Informatics Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
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9
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Marcotte H, Cao Y, Zuo F, Simonelli L, Sammartino JC, Pedotti M, Sun R, Cassaniti I, Hagbom M, Piralla A, Yang J, Du L, Percivalle E, Bertoglio F, Schubert M, Abolhassani H, Sherina N, Guerra C, Borte S, Rezaei N, Kumagai-Braesch M, Xue Y, Su C, Yan Q, He P, Grönwall C, Klareskog L, Calzolai L, Cavalli A, Wang Q, Robbiani DF, Hust M, Shi Z, Feng L, Svensson L, Chen L, Bao L, Baldanti F, Xiao J, Qin C, Hammarström L, Yang X, Varani L, Xie XS, Pan-Hammarström Q. Conversion of monoclonal IgG to dimeric and secretory IgA restores neutralizing ability and prevents infection of Omicron lineages. Proc Natl Acad Sci U S A 2024; 121:e2315354120. [PMID: 38194459 PMCID: PMC10801922 DOI: 10.1073/pnas.2315354120] [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: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 01/11/2024] Open
Abstract
The emergence of Omicron lineages and descendent subvariants continues to present a severe threat to the effectiveness of vaccines and therapeutic antibodies. We have previously suggested that an insufficient mucosal immunoglobulin A (IgA) response induced by the mRNA vaccines is associated with a surge in breakthrough infections. Here, we further show that the intramuscular mRNA and/or inactivated vaccines cannot sufficiently boost the mucosal secretory IgA response in uninfected individuals, particularly against the Omicron variant. We thus engineered and characterized recombinant monomeric, dimeric, and secretory IgA1 antibodies derived from four neutralizing IgG monoclonal antibodies (mAbs 01A05, rmAb23, DXP-604, and XG014) targeting the receptor-binding domain of the spike protein. Compared to their parental IgG antibodies, dimeric and secretory IgA1 antibodies showed a higher neutralizing activity against different variants of concern (VOCs), in part due to an increased avidity. Importantly, the dimeric or secretory IgA1 form of the DXP-604 antibody significantly outperformed its parental IgG antibody, and neutralized the Omicron lineages BA.1, BA.2, and BA.4/5 with a 25- to 75-fold increase in potency. In human angiotensin converting enzyme 2 (ACE2) transgenic mice, a single intranasal dose of the dimeric IgA DXP-604 conferred prophylactic and therapeutic protection against Omicron BA.5. Thus, dimeric or secretory IgA delivered by nasal administration may potentially be exploited for the treatment and prevention of Omicron infection, thereby providing an alternative tool for combating immune evasion by the current circulating subvariants and, potentially, future VOCs.
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Affiliation(s)
- Harold Marcotte
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm17165, Sweden
| | - Yunlong Cao
- Changping Laboratory, Beijing102206, People’s Republic of China
- School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing100871, People’s Republic of China
| | - Fanglei Zuo
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm17165, Sweden
| | - Luca Simonelli
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona6500, Switzerland
| | - Josè Camilla Sammartino
- Microbiology and Virology Department, Fondazione Istituto di ricovero e cura a carattere scientifico (IRCCS) Policlinico San Matteo, Pavia27100, Italy
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona6500, Switzerland
| | - Rui Sun
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm17165, Sweden
| | - Irene Cassaniti
- Microbiology and Virology Department, Fondazione Istituto di ricovero e cura a carattere scientifico (IRCCS) Policlinico San Matteo, Pavia27100, Italy
| | - Marie Hagbom
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping 58185, Sweden
| | - Antonio Piralla
- Microbiology and Virology Department, Fondazione Istituto di ricovero e cura a carattere scientifico (IRCCS) Policlinico San Matteo, Pavia27100, Italy
| | - Jinxuan Yang
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming650023, People’s Republic of China
| | - Likun Du
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm17165, Sweden
| | - Elena Percivalle
- Microbiology and Virology Department, Fondazione Istituto di ricovero e cura a carattere scientifico (IRCCS) Policlinico San Matteo, Pavia27100, Italy
| | - Federico Bertoglio
- Department of Medical Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig38106, Germany
| | - Maren Schubert
- Department of Medical Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig38106, Germany
| | - Hassan Abolhassani
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm17165, Sweden
| | - Natalia Sherina
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm17165, Sweden
| | - Concetta Guerra
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona6500, Switzerland
| | - Stephan Borte
- Department of Laboratory Medicine, Hospital St. Georg, Leipzig04129, Germany
- ImmunoDeficiencyCenter Leipzig, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiency Diseases, Hospital St. Georg, Leipzig04129, Germany
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran University of Medical Sciences, Tehran14194, Iran
| | - Makiko Kumagai-Braesch
- Division of Transplantation Surgery, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm14186, Sweden
| | - Yintong Xue
- Department of Immunology, Peking University Health Science Center, Beijing100191, People’s Republic of China
| | - Chen Su
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, People’s Republic of China
| | - Qihong Yan
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences,Guangzhou510530, People’s Republic of China
| | - Ping He
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences,Guangzhou510530, People’s Republic of China
| | - Caroline Grönwall
- Division of Rheumatology, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm17176, Sweden
| | - Lars Klareskog
- Division of Rheumatology, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm17176, Sweden
- Rheumatology Unit, Karolinska University Hospital, Stockholm17176, Sweden
| | - Luigi Calzolai
- European Commission, Joint Research Centre, Ispra21027, Italy
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona6500, Switzerland
| | - Qiao Wang
- Key Laboratory of Medical Molecular Virology (Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, 200032 Shanghai200032, People’s Republic of China
| | - Davide F. Robbiani
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona6500, Switzerland
| | - Michael Hust
- Department of Medical Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig38106, Germany
| | - Zhengli Shi
- State Key laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei430071, People’s Republic of China
| | - Liqiang Feng
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences,Guangzhou510530, People’s Republic of China
| | - Lennart Svensson
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping 58185, Sweden
- Division of Infectious Diseases, Department of Medicine, Karolinska Institute, Stockholm17177, Sweden
| | - Ling Chen
- Guangzhou Laboratory, Guangzhou510005, People’s Republic of China
| | - Linlin Bao
- Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, National Health Commission Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing100021, People’s Republic of China
- National Center of Technology Innovation for Animal Model, Beijing102206, People’s Republic of China
| | - Fausto Baldanti
- Microbiology and Virology Department, Fondazione Istituto di ricovero e cura a carattere scientifico (IRCCS) Policlinico San Matteo, Pavia27100, Italy
- Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia27100, Italy
| | - Junyu Xiao
- Changping Laboratory, Beijing102206, People’s Republic of China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, People’s Republic of China
| | - Chuan Qin
- Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, National Health Commission Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing100021, People’s Republic of China
- National Center of Technology Innovation for Animal Model, Beijing102206, People’s Republic of China
| | - Lennart Hammarström
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm17165, Sweden
| | - Xinglou Yang
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming650023, People’s Republic of China
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona6500, Switzerland
| | - Xiaoliang Sunney Xie
- Changping Laboratory, Beijing102206, People’s Republic of China
- School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing100871, People’s Republic of China
| | - Qiang Pan-Hammarström
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm17165, Sweden
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10
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Kodsi IA, Rayes DE, Koweyes J, Khoury CA, Rahy K, Thoumi S, Chamoun M, Haddad H, Mokhbat J, Tokajian S. Tracking SARS-CoV-2 variants during the 2023 flu season and beyond in Lebanon. Virus Res 2024; 339:199289. [PMID: 38036064 PMCID: PMC10704499 DOI: 10.1016/j.virusres.2023.199289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/12/2023] [Accepted: 11/27/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND Early SARS-CoV-2 variant detection relies on testing and genomic surveillance. The Omicron variant (B.1.1.529) has quickly become the dominant type among the previous circulating variants worldwide. Several subvariants have emerged exhibiting greater infectivity and immune evasion. In this study we aimed at studying the prevalence of the Omicron subvariants during the flu season and beyond in Lebanon through genomic screening and at determining the overall standing and trajectory of the pandemic in the country. METHODS A total of 155 SARS-CoV-2 RNA samples were sequenced, using Nanopore sequencing technology. RESULTS Nanopore sequencing of 155 genomes revealed their distribution over 39 Omicron variants. XBB.1.5 (23.29 %) was the most common, followed by XBB.1.9.1 (10.96 %) and XBB.1.42 (7.5 %). The first batch collected between September and November 2022, included the BA.2.75.2, BA.5.2, BA.5.2.20, BA.5.2.25 and BQ.1.1.5 lineages. Between December 2022 and January 2023, those lineages were replaced by BA.2.75.5, BN.1, BN.1.4, BQ.1, BQ.1.1, BQ.1.1.23, CH.1.1, CM.4 and XBK. Starting February 2023, we observed a gradual emergence and dominance of the recombinant XBB and its sub-lineages (XBB.1, XBB.1.5, XBB.1.5.2, XBB.1.5.3, XBB.1.9, XBB.1.9.1, XBB.1.9.2, XBB.1.16, XBB.1.22 and XBB.1.42). CONCLUSIONS The timely detection and characterization of SARS-CoV-2 variants is important to reduce transmission through established disease control measures and to avoid introductions into animal populations that could lead to serious public health implications.
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Affiliation(s)
- Ibrahim Al Kodsi
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Douaa El Rayes
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Jad Koweyes
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Charbel Al Khoury
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Kelven Rahy
- School of Medicine, Lebanese American University, Lebanon
| | - Sergio Thoumi
- Department of Computer Science and Mathematics, School of Arts and Sciences, Lebanese American University, Lebanon
| | | | - Hoda Haddad
- Clinical Microbiology laboratory, Lebanese American University Medical Center Rizk Hospital, Beirut, Lebanon
| | - Jacques Mokhbat
- Clinical Microbiology laboratory, Lebanese American University Medical Center Rizk Hospital, Beirut, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon.
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11
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Wang E, Yang QJ, Xu XX, Zou QC, Long Y, Ma G, Deng ZH, Zhao JB, Li MH, Zeng J. Differential pathogenic and molecular features in neurological infection of SARS-CoV-2 Omicron BA.5.2 and BA.2.75 and Delta. J Med Virol 2024; 96:e29357. [PMID: 38235532 DOI: 10.1002/jmv.29357] [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: 07/31/2023] [Revised: 11/07/2023] [Accepted: 12/17/2023] [Indexed: 01/19/2024]
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a global threat, exacerbated by the emergence of viral variants. Two variants of SARS-CoV-2, Omicron BA.2.75 and BA.5, led to global infection peaks between May 2022 and May 2023, yet their precise characteristics in pathogenesis are not well understood. In this study, we compared these two Omicron sublineages with the previously dominant Delta variant using a human angiotensin-converting enzyme 2 knock-in mouse model. As expected, Delta exhibited higher viral replication in the lung and brain than both Omicron sublineages which induced less severe lung damage and immune activation. In contrast, the Omicron variants especially BA.5.2 showed a propensity for cellular proliferation and developmental pathways. Both Delta and BA.5.2 variants, but not BA.2.75, led to decreased pulmonary lymphocytes, indicating differential adaptive immune response. Neuroinvasiveness was shared with all strains, accompanied by vascular abnormalities, synaptic injury, and loss of astrocytes. However, Immunostaining assays and transcriptomic analysis showed that BA.5.2 displayed stronger immune suppression and neurodegeneration, while BA.2.75 exhibited more similar characteristics to Delta in the cortex. Such differentially infectious features could be partially attributed to the weakened interaction between Omicron Spike protein and host proteomes decoded via co-immunoprecipitation followed by mass spectrometry in neuronal cells. Our present study supports attenuated replication and pathogenicity of Omicron variants but also highlights their newly infectious characteristics in the lung and brain, especially with BA.5.2 demonstrating enhanced immune evasion and neural damage that could exacerbate neurological sequelae.
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Affiliation(s)
- Erlin Wang
- Songjiang Research Institute, Songjiang Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Qiao-Jiang Yang
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xiang-Xiong Xu
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Qing-Cui Zou
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yanghaopeng Long
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Guanqin Ma
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhong-Hua Deng
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jie-Bin Zhao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ming-Hua Li
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jianxiong Zeng
- Songjiang Research Institute, Songjiang Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, China
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12
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Wang Q, Guo Y, Liu L, Schwanz LT, Li Z, Nair MS, Ho J, Zhang RM, Iketani S, Yu J, Huang Y, Qu Y, Valdez R, Lauring AS, Huang Y, Gordon A, Wang HH, Liu L, Ho DD. Antigenicity and receptor affinity of SARS-CoV-2 BA.2.86 spike. Nature 2023; 624:639-644. [PMID: 37871613 DOI: 10.1038/s41586-023-06750-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023]
Abstract
A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariant, BA.2.86, has emerged and spread to numerous countries worldwide, raising alarm because its spike protein contains 34 additional mutations compared with its BA.2 predecessor1. We examined its antigenicity using human sera and monoclonal antibodies (mAbs). Reassuringly, BA.2.86 was no more resistant to human sera than the currently dominant XBB.1.5 and EG.5.1, indicating that the new subvariant would not have a growth advantage in this regard. Importantly, sera from people who had XBB breakthrough infection exhibited robust neutralizing activity against all viruses tested, suggesting that upcoming XBB.1.5 monovalent vaccines could confer added protection. Although BA.2.86 showed greater resistance to mAbs to subdomain 1 (SD1) and receptor-binding domain (RBD) class 2 and 3 epitopes, it was more sensitive to mAbs to class 1 and 4/1 epitopes in the 'inner face' of the RBD that is exposed only when this domain is in the 'up' position. We also identified six new spike mutations that mediate antibody resistance, including E554K that threatens SD1 mAbs in clinical development. The BA.2.86 spike also had a remarkably high receptor affinity. The ultimate trajectory of this new SARS-CoV-2 variant will soon be revealed by continuing surveillance, but its worldwide spread is worrisome.
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Affiliation(s)
- Qian Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yicheng Guo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Liyuan Liu
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Logan T Schwanz
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Pathobiology and Mechanisms of Disease, Columbia University Irving Medical Center, New York, NY, USA
| | - Zhiteng Li
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jerren Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Richard M Zhang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jian Yu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yiming Huang
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yiming Qu
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Riccardo Valdez
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Adam S Lauring
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Aubree Gordon
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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Liu S, Liang Z, Nie J, Gao WB, Li X, Zhang L, Yu Y, Wang Y, Huang W. Sera from breakthrough infections with SARS-CoV-2 BA.5 or BF.7 showed lower neutralization activity against XBB.1.5 and CH.1.1. Emerg Microbes Infect 2023; 12:2225638. [PMID: 37313604 PMCID: PMC10339773 DOI: 10.1080/22221751.2023.2225638] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/11/2023] [Indexed: 06/15/2023]
Abstract
From December 2022 to January 2023, SARS-CoV-2 infections caused by BA.5 and BF.7 subvariants of B.1.1.529 (Omicron) spread in China. It is urgently needed to evaluate the protective immune responses in the infected individuals against the current circulating variants to predict the future potential infection waves, such as the BQ.1.1, XBB.1.5, and CH1.1 variants. In this study, we constructed a panel of pseudotyped viruses for SARS-CoV-2 for the past and current circulating variants, including D614G, Delta, BA.1, BA.5, BF.7, BQ.1.1, XBB.1.5 and CH.1.1. We investigated the neutralization sensitivity of these pseudotyped viruses to sera from individuals who had BA.5 or BF.7 breakthrough infections in the infection wave of last December in China. The mean neutralization ID50 against infected variants BA.5 and BF.7 are 533 and 444, respectively. The highest neutralizing antibody level was observed when tested against the D614G strain, with the ID50 of 742, which is about 1.52-folds higher than that against the BA.5/BF.7 variant. The ID50 for BA.1, Delta, and BQ.1.1 pseudotyped viruses were about 2-3 folds lower when compared to BA.5/BF.7. The neutralization activities of these serum samples against XBB.1.5 and CH.1.1 decreased 7.39-folds and 15.25-folds when compared to that against BA.5/BF.7. The immune escape capacity of these two variants might predict new infection waves in future when the neutralizing antibody levels decrease furtherly.
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Affiliation(s)
- Shuo Liu
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Changping Laboratory, Beijing, People’s Republic of China
| | - Ziteng Liang
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People’s Republic of China
| | - Jianhui Nie
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People’s Republic of China
| | - Wei bo Gao
- Department of Emergency, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Xinyi Li
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, People’s Republic of China
| | - Li Zhang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People’s Republic of China
| | - Yuanling Yu
- Changping Laboratory, Beijing, People’s Republic of China
| | - Youchun Wang
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Changping Laboratory, Beijing, People’s Republic of China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People’s Republic of China
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14
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Chen C, Wang X, Zhang Z. Humoral and cellular immunity against diverse SARS-CoV-2 variants. J Genet Genomics 2023; 50:934-947. [PMID: 37865193 DOI: 10.1016/j.jgg.2023.10.003] [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: 06/29/2023] [Revised: 09/27/2023] [Accepted: 10/10/2023] [Indexed: 10/23/2023]
Abstract
Since the outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019, the virus has rapidly spread worldwide. This has led to an unprecedented global pandemic, marked by millions of COVID-19 cases and a significant number of fatalities. Over a relatively short period, several different vaccine platforms are developed and deployed for use globally to curb the pandemic. However, the genome of SARS-CoV-2 continuously undergoes mutation and/or recombination, resulting in the emergence of several variants of concern (VOC). These VOCs can elevate viral transmission and evade the neutralizing antibodies induced by vaccines, leading to reinfections. Understanding the impact of the SARS-CoV-2 genomic mutation on viral pathogenesis and immune escape is crucial for assessing the threat of new variants to public health. This review focuses on the emergence and pathogenesis of VOC, with particular emphasis on their evasion of neutralizing antibodies. Furthermore, the memory B cell, CD4+, and CD8+ T cell memory induced by different COVID-19 vaccines or infections are discussed, along with how these cells recognize VOC. This review summarizes the current knowledge on adaptive immunology regarding SARS-CoV-2 infection and vaccines. Such knowledge may also be applied to vaccine design for other pathogens.
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Affiliation(s)
- Changxu Chen
- Center for Infectious Disease Research, School of Life Science, Westlake University, Hangzhou, Zhejiang 310001, China
| | - Xin Wang
- Center for Infectious Disease Research, School of Life Science, Westlake University, Hangzhou, Zhejiang 310001, China
| | - Zeli Zhang
- Center for Infectious Disease Research, School of Life Science, Westlake University, Hangzhou, Zhejiang 310001, China.
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15
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Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Accurate Characterization of Conformational Ensembles and Binding Mechanisms of the SARS-CoV-2 Omicron BA.2 and BA.2.86 Spike Protein with the Host Receptor and Distinct Classes of Antibodies Using AlphaFold2-Augmented Integrative Computational Modeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.18.567697. [PMID: 38045395 PMCID: PMC10690158 DOI: 10.1101/2023.11.18.567697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The latest wave SARS-CoV-2 Omicron variants displayed a growth advantage and the increased viral fitness through convergent evolution of functional hotspots that work synchronously to balance fitness requirements for productive receptor binding and efficient immune evasion. In this study, we combined AlphaFold2-based structural modeling approaches with all-atom MD simulations and mutational profiling of binding energetics and stability for prediction and comprehensive analysis of the structure, dynamics, and binding of the SARS-CoV-2 Omicron BA.2.86 spike variant with ACE2 host receptor and distinct classes of antibodies. We adapted several AlphaFold2 approaches to predict both structure and conformational ensembles of the Omicron BA.2.86 spike protein in the complex with the host receptor. The results showed that AlphaFold2-predicted conformational ensemble of the BA.2.86 spike protein complex can accurately capture the main dynamics signatures obtained from microscond molecular dynamics simulations. The ensemble-based dynamic mutational scanning of the receptor binding domain residues in the BA.2 and BA.2.86 spike complexes with ACE2 dissected the role of the BA.2 and BA.2.86 backgrounds in modulating binding free energy changes revealing a group of conserved hydrophobic hotspots and critical variant-specific contributions of the BA.2.86 mutational sites R403K, F486P and R493Q. To examine immune evasion properties of BA.2.86 in atomistic detail, we performed large scale structure-based mutational profiling of the S protein binding interfaces with distinct classes of antibodies that displayed significantly reduced neutralization against BA.2.86 variant. The results quantified specific function of the BA.2.86 mutations to ensure broad resistance against different classes of RBD antibodies. This study revealed the molecular basis of compensatory functional effects of the binding hotspots, showing that BA.2.86 lineage may have primarily evolved to improve immune escape while modulating binding affinity with ACE2 through cooperative effect of R403K, F486P and R493Q mutations. The study supports a hypothesis that the impact of the increased ACE2 binding affinity on viral fitness is more universal and is mediated through cross-talk between convergent mutational hotspots, while the effect of immune evasion could be more variant-dependent.
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16
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Bhattacharya M, Chatterjee S, Lee SS, Dhama K, Chakraborty C. Antibody evasion associated with the RBD significant mutations in several emerging SARS-CoV-2 variants and its subvariants. Drug Resist Updat 2023; 71:101008. [PMID: 37757651 DOI: 10.1016/j.drup.2023.101008] [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: 01/18/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023]
Abstract
Since the origin of the wild strain of SARS-CoV-2, several variants have emerged, which were designated as VOC, VOI, and VUM from time to time. The Omicron variant is noted as the recent VOC. After the origin of the Omicron variant on November 2021, several subvariants of Omicron have originated subsequently, like BA.1/2, BA.2.75/2.75.2, BA.4/5, BF.7, BQ.1/1.1, XBB.1/1.5, etc. which are circulated throughout the globe. Scientists reported that antibody escape is a common phenomenon observed in all the previous VOCs, VOIs, including Omicron and its subvariants. The mutations in the NTD (N-terminal domain) and RBD (Receptor-binding domain) of the spike of these variants and subvariants are responsible for antibody escape. At the same time, it has been noted that spike RBD mutations have been increasing in the last few months. This review illustrates significant RBD mutations namely R346T, K417N/T, L452R, N460K E484A/K/Q, and N501Y found in the previous emerging SARS-CoV-2 variants, including Omicron and its subvariants in high frequency and their role in antibody evasion and immune evasion. The review also describes the different classes of nAb responsible for antibody escape in SARS-CoV-2 variants and the molecular perspective of the mutation in nAb escape. It will help the future researchers to develop efficient vaccines which can finally prevent the pandemic.
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Affiliation(s)
- Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Srijan Chatterjee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, Republic of Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, Republic of Korea
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata 700126, West Bengal, India.
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17
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Faraone JN, Qu P, Zheng YM, Carlin C, Jones D, Panchal AR, Saif LJ, Oltz EM, Gumina RJ, Liu SL. Continued evasion of neutralizing antibody response by Omicron XBB.1.16. Cell Rep 2023; 42:113193. [PMID: 37777967 PMCID: PMC10872815 DOI: 10.1016/j.celrep.2023.113193] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/17/2023] [Accepted: 09/15/2023] [Indexed: 10/03/2023] Open
Abstract
The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to challenge the efficacy of vaccination efforts against coronavirus disease 2019 (COVID-19). The Omicron XBB lineage of SARS-CoV-2 has presented dramatic evasion of neutralizing antibodies stimulated by mRNA vaccination and COVID-19 convalescence. XBB.1.16, characterized by two mutations relative to the dominating variant XBB.1.5, i.e., E180V and K478R, has been on the rise globally. In this study, we compare the immune escape of XBB.1.16 with XBB.1.5, alongside ancestral variants D614G, BA.2, and BA.4/5. We demonstrate that XBB.1.16 is strongly immune evasive, with extent comparable to XBB.1.5 in bivalent-vaccinated healthcare worker sera, 3-dose-vaccinated healthcare worker sera, and BA.4/5-wave convalescent sera. Interestingly, the XBB.1.16 spike is less fusogenic than that of XBB.1.5, and this phenotype requires both E180V and K478R mutations to manifest. Overall, our findings emphasize the importance of the continued surveillance of variants and the need for updated mRNA vaccine formulations.
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Affiliation(s)
- Julia N Faraone
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Panke Qu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Yi-Min Zheng
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Claire Carlin
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel Jones
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Ashish R Panchal
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Linda J Saif
- Center for Food Animal Health, Animal Sciences Department, OARDC, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; Veterinary Preventive Medicine Department, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA; Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Eugene M Oltz
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Richard J Gumina
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA; Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA.
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18
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Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Comparative Analysis of Conformational Dynamics and Systematic Characterization of Cryptic Pockets in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB.1 Spike Complexes with the ACE2 Host Receptor: Confluence of Binding and Structural Plasticity in Mediating Networks of Conserved Allosteric Sites. Viruses 2023; 15:2073. [PMID: 37896850 PMCID: PMC10612107 DOI: 10.3390/v15102073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
In the current study, we explore coarse-grained simulations and atomistic molecular dynamics together with binding energetics scanning and cryptic pocket detection in a comparative examination of conformational landscapes and systematic characterization of allosteric binding sites in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB.1 spike full-length trimer complexes with the host receptor ACE2. Microsecond simulations, Markov state models and mutational scanning of binding energies of the SARS-CoV-2 BA.2 and BA.2.75 receptor binding domain complexes revealed the increased thermodynamic stabilization of the BA.2.75 variant and significant dynamic differences between these Omicron variants. Molecular simulations of the SARS-CoV-2 Omicron spike full-length trimer complexes with the ACE2 receptor complemented atomistic studies and enabled an in-depth analysis of mutational and binding effects on conformational dynamic and functional adaptability of the Omicron variants. Despite considerable structural similarities, Omicron variants BA.2, BA.2.75 and XBB.1 can induce unique conformational dynamic signatures and specific distributions of the conformational states. Using conformational ensembles of the SARS-CoV-2 Omicron spike trimer complexes with ACE2, we conducted a comprehensive cryptic pocket screening to examine the role of Omicron mutations and ACE2 binding on the distribution and functional mechanisms of the emerging allosteric binding sites. This analysis captured all experimentally known allosteric sites and discovered networks of inter-connected and functionally relevant allosteric sites that are governed by variant-sensitive conformational adaptability of the SARS-CoV-2 spike structures. The results detailed how ACE2 binding and Omicron mutations in the BA.2, BA.2.75 and XBB.1 spike complexes modulate the distribution of conserved and druggable allosteric pockets harboring functionally important regions. The results are significant for understanding the functional roles of druggable cryptic pockets that can be used for allostery-mediated therapeutic intervention targeting conformational states of the Omicron variants.
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Affiliation(s)
- Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
| | - Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX 75275, USA; (S.X.); (P.T.)
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX 75275, USA; (S.X.); (P.T.)
| | - Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
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19
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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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20
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Pondé RADA. Physicochemical effects of emerging exchanges on the spike protein's RBM of the SARS-CoV-2 Omicron subvariants BA.1-BA.5 and its influence on the biological properties and attributes developed by these subvariants. Virology 2023; 587:109850. [PMID: 37562286 DOI: 10.1016/j.virol.2023.109850] [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: 04/24/2023] [Revised: 06/13/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
Emerging in South Africa, SARS-CoV-2 Omicron variant was marked by the expression of an exaggerated number of mutations throughout its genome and by the emergence of subvariants, whose attributes developed by them have been associated with amino acid exchanges that occur mainly in the RBM region of the spike protein. The RBM comprises a region within the RBD and is directly involved in the SARS-CoV-2 spike protein interaction with the host cell ACE2 receptor, during the infection mechanism and viral transmission. Defined as the region from aa 437 to aa 508, there are several residues in certain positions that interact directly with the human ACE-2 receptor during these processes. The occurrence of amino acid exchanges in these positions causes physicochemical alterations in the SARS-CoV-2 spike protein, which confer additional advantages and attributes to the agent. In addition, these exchanges serve as a basis for the characterization of new variants and subvariants of SARS-CoV-2. In this review, the amino acid exchanges that have occurred in the RBM of the subvariants BA.1 to BA.5 of SARS-CoV-2 that emerged from the Omicron are described. The physicochemical effects caused by them on spike protein are also described, as well as their influence on the biological properties and attributes developed by the subvariants BA.1, BA.2, BA.3, BA.4 and BA.5.
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Affiliation(s)
- Robério Amorim de Almeida Pondé
- Secretaria de Estado da Saúde -SES/Superintendência de Vigilância em Saúde-SUVISA/GO, Gerência de Vigilância Epidemiológica de Doenças Transmissíveis-GVEDT/Coordenação de Análises e Pesquisas-CAP, Goiânia, Goiás, Brazil; Laboratory of Human Virology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil.
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21
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Wang L, Wang Y, Zhou H. Potent antibodies against immune invasive SARS-CoV-2 Omicron subvariants. Int J Biol Macromol 2023; 249:125997. [PMID: 37499711 DOI: 10.1016/j.ijbiomac.2023.125997] [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: 04/27/2023] [Revised: 07/23/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
The development of neutralizing antibodies (nAbs) is an important strategy to tackle the Omicron variant. Omicron N-terminal domain (NTD) mutations including A67V, G142D, and N212I alter the antigenic structure, and mutations in the spike (S) receptor binding domain (RBD), such as N501Y, R346K, and T478K enhance affinity between the RBD and angiotensin-converting enzyme 2 (ACE2), thus conferring Omicron powerful immune evasion. Most nAbs (COV2-2130, ZCB11, REGN10933) and combinations of nAbs (COV2-2196 + COV2-2130, REGN10933 + REGN10987, Brii-196 + Brii-198) have either greatly reduced or lost their neutralizing ability against Omicron, but several nAbs such as SA55, SA58, S309, LY-CoV1404 are still effective in neutralizing most Omicron subvariants. This paper focuses on Omicron subvariants mutations and mechanisms of current therapeutic antibodies that remain efficacious against Omicron subvariants, which will guide us in exploring a new generation of broad nAbs as key therapeutics to tackle SARS-CoV-2 and accelerate the exploration of novel clinical antiviral reagents.
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Affiliation(s)
- Lidong Wang
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yang Wang
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Hao Zhou
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chongqing Traditional Chinese Medicine Hospital, Chongqing 400016, China.
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22
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Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Examining Functional Linkages Between Conformational Dynamics, Protein Stability and Evolution of Cryptic Binding Pockets in the SARS-CoV-2 Omicron Spike Complexes with the ACE2 Host Receptor: Recombinant Omicron Variants Mediate Variability of Conserved Allosteric Sites and Binding Epitopes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.11.557205. [PMID: 37745525 PMCID: PMC10515794 DOI: 10.1101/2023.09.11.557205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
In the current study, we explore coarse-grained simulations and atomistic molecular dynamics together with binding energetics scanning and cryptic pocket detection in a comparative examination of conformational landscapes and systematic characterization of allosteric binding sites in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB.1 spike full-length trimer complexes with the host receptor ACE2. Microsecond simulations, Markov state models and mutational scanning of binding energies of the SARS-CoV-2 BA.2 and BA.2.75 receptor binding domain complexes revealed the increased thermodynamic stabilization of the BA.2.75 variant and significant dynamic differences between these Omicron variants. Molecular simulations of the SARS-CoV-2 Omicron spike full length trimer complexes with the ACE2 receptor complemented atomistic studies and enabled an in-depth analysis of mutational and binding effects on conformational dynamic and functional adaptability of the Omicron variants. Despite considerable structural similarities, Omicron variants BA.2, BA.2.75 and XBB.1 can induce unique conformational dynamic signatures and specific distributions of the conformational states. Using conformational ensembles of the SARS-CoV-2 Omicron spike trimer complexes with ACE2, we conducted a comprehensive cryptic pocket screening to examine the role of Omicron mutations and ACE2 binding on the distribution and functional mechanisms of the emerging allosteric binding sites. This analysis captured all experimentally known allosteric sites and discovered networks of inter-connected and functionally relevant allosteric sites that are governed by variant-sensitive conformational adaptability of the SARS-CoV-2 spike structures. The results detailed how ACE2 binding and Omicron mutations in the BA.2, BA.2.75 and XBB.1 spike complexes modulate the distribution of conserved and druggable allosteric pockets harboring functionally important regions. The results of are significant for understanding functional roles of druggable cryptic pockets that can be used for allostery-mediated therapeutic intervention targeting conformational states of the Omicron variants.
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23
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Kong X, Gao P, Jiang Y, Lu L, Zhao M, Liu Y, Deng G, Zhu H, Cao Y, Ma L. Discrimination of SARS-CoV-2 omicron variant and its lineages by rapid detection of immune-escape mutations in spike protein RBD using asymmetric PCR-based melting curve analysis. Virol J 2023; 20:192. [PMID: 37626353 PMCID: PMC10463914 DOI: 10.1186/s12985-023-02137-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 07/22/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND The SARS-CoV-2 Omicron strain has multiple immune-escape mutations in the spike protein receptor-binding domain (RBD). Rapid detection of these mutations to identify Omicron and its lineages is essential for guiding public health strategies and patient treatments. We developed a two-tube, four-color assay employing asymmetric polymerase chain reaction (PCR)-based melting curve analysis to detect Omicron mutations and discriminate the BA.1, BA.2, BA.4/5, and BA.2.75 lineages. METHODS The presented technique involves combinatory analysis of the detection of six fluorescent probes targeting the immune-escape mutations L452R, N460K, E484A, F486V, Q493R, Q498R, and Y505H within one amplicon in the spike RBD and probes targeting the ORF1ab and N genes. After protocol optimization, the analytical performance of the technique was evaluated using plasmid templates. Sensitivity was assessed based on the limit of detection (LOD), and reliability was assessed by calculating the intra- and inter-run precision of melting temperatures (Tms). Specificity was assessed using pseudotyped lentivirus of common human respiratory pathogens and human genomic DNA. The assay was used to analyze 40 SARS-CoV-2-positive clinical samples (including 36 BA.2 and 4 BA.4/5 samples) and pseudotyped lentiviruses of wild-type and BA.1 viral RNA control materials, as well as 20 SARS-CoV-2-negative clinical samples, and its accuracy was evaluated by comparing the results with those of sequencing. RESULTS All genotypes were sensitively identified using the developed method with a LOD of 39.1 copies per reaction. The intra- and inter-run coefficients of variation for the Tms were ≤ 0.69% and ≤ 0.84%, with standard deviations ≤ 0.38 °C and ≤ 0.41 °C, respectively. Validation of the assay using known SARS-CoV-2-positive samples demonstrated its ability to correctly identify the targeted mutations and preliminarily characterize the Omicron lineages. CONCLUSION The developed assay can provide accurate, reliable, rapid, simple and low-cost detection of the immune-escape mutations located in the spike RBD to detect the Omicron variant and discriminate its lineages, and its use can be easily generalized in clinical laboratories with a fluorescent PCR platform.
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Affiliation(s)
- Xiaomu Kong
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Peng Gao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Yongwei Jiang
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Lixia Lu
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Meimei Zhao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Yi Liu
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Guoxiong Deng
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Haoyan Zhu
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Yongtong Cao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China.
| | - Liang Ma
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China.
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24
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Holland SC, Holland LA, Smith MF, Lee MB, Hu JC, Lim ES. Digital PCR Discriminates between SARS-CoV-2 Omicron Variants and Immune Escape Mutations. Microbiol Spectr 2023; 11:e0525822. [PMID: 37306573 PMCID: PMC10434287 DOI: 10.1128/spectrum.05258-22] [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: 12/21/2022] [Accepted: 05/10/2023] [Indexed: 06/13/2023] Open
Abstract
As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, mutations arise that will allow the virus to evade immune defenses and therapeutics. Assays that can identify these mutations can be used to guide personalized patient treatment plans. Digital PCR (dPCR) is a fast and reliable complement to whole-genome sequencing that can be used to discriminate single nucleotide polymorphisms (SNPs) in template molecules. Here, we developed a panel of SARS-CoV-2 dPCR assays and demonstrate its applications for typing variant lineages and therapeutic monoclonal antibody resistance. We first designed multiplexed dPCR assays for SNPs located at residue 3395 in the orf1ab gene that differentiate the Delta, Omicron BA.1, and Omicron BA.2 lineages. We demonstrate their effectiveness on 596 clinical saliva specimens that were sequence verified using Illumina whole-genome sequencing. Next, we developed dPCR assays for spike mutations R346T, K444T, N460K, F486V, and F486S, which are associated with host immune evasion and reduced therapeutic monoclonal antibody efficacy. We demonstrate that these assays can be run individually or multiplexed to detect the presence of up to 4 SNPs in a single assay. We perform these dPCR assays on 81 clinical saliva SARS-CoV-2-positive specimens and properly identify mutations in Omicron subvariants BA.2.75.2, BM.1.1, BN.1, BF.7, BQ.1, BQ.1.1, and XBB. Thus, dPCR could serve as a useful tool to determine if clinical specimens contain therapeutically relevant mutations and inform patient treatment. IMPORTANCE Spike mutations in the SARS-CoV-2 genome confer resistance to therapeutic monoclonal antibodies. Authorization for treatment options is typically guided by general trends of variant prevalence. For example, bebtelovimab is no longer authorized for emergency use in the United States due to the increased prevalence of antibody-resistant BQ.1, BQ.1.1, and XBB Omicron subvariants. However, this blanket approach limits access to life-saving treatment options to patients who are otherwise infected with susceptible variants. Digital PCR assays targeting specific mutations can complement whole-genome sequencing approaches to genotype the virus. In this study, we demonstrate the proof of concept that dPCR can be used to type lineage defining and monoclonal antibody resistance-associated mutations in saliva specimens. These findings show that digital PCR could be used as a personalized diagnostic tool to guide individual patient treatment.
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Affiliation(s)
- Steven C. Holland
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - LaRinda A. Holland
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Matthew F. Smith
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mihyun B. Lee
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - James C. Hu
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Efrem S. Lim
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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25
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Li W, Zhao T, Tao B, Zhao L, Xiao H, Ding X, Li C, Chen L, Cheng H, Lou Y, Chen Y, Wu C. Monovalent Omicron COVID-19 vaccine triggers superior neutralizing antibody responses against Omicron subvariants than Delta and Omicron bivalent vaccine. Hum Vaccin Immunother 2023; 19:2264589. [PMID: 37846840 PMCID: PMC10583637 DOI: 10.1080/21645515.2023.2264589] [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: 07/06/2023] [Accepted: 09/26/2023] [Indexed: 10/18/2023] Open
Abstract
The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants poses a challenge to determine the optimal updated composition of the coronavirus disease 2019 (COVID-19) vaccine. The present study aimed to investigate the immunogenicity of the Delta monovalent vaccine, the Omicron monovalent vaccine, and the Delta and Omicron BA.1 bivalent vaccine. Three COVID-19 vaccines were designed using the heterologous DNA prime-protein boost strategy, with each vaccine containing either Delta receptor-binding domain (RBD) of the spike protein, Omicron RBD, or both Delta and Omicron antigens. Temporal serum antibody binding titers and neutralizing antibody titers induced by the three vaccines in New Zealand White rabbits were analyzed. To further dissect the vaccine elicited antibodies (mAb) responses at the molecular level, a panel of rabbit monoclonal antibodies (RmAbs) was generated by a high-throughput single B cell sorting and discovery pipeline and further comprehensively characterized. The Omicron monovalent vaccine induced higher antibody binding titers and neutralization activities than the Delta and Omicron bivalent vaccine. Four RmAbs with robust neutralization capacity were isolated from rabbits immunized with the Omicron or Delta monovalent vaccine. Notably, 9E11 isolated from the Omicron monovalent vaccine group neutralized all the Omicron subvariants with an IC50 value ranging from 1.5 to 503.6 ng/mL; thus, this vaccine could serve as a prophylactic and therapeutic intervention. Given the increasing incidence of COVID-19 cases due to the Omicron variant, RBD from the Omicron strain could serve as a candidate immunogen that can induce higher neutralization activities against the SARS-CoV-2 Omicron sublineages.
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Affiliation(s)
- Wanting Li
- Department of Infectious Diseases, Nanjing Drum Tower Hospital Clinical College of Xuzhou Medical University, Nanjing, Jiangsu, China
| | - Tiantian Zhao
- Department of Infectious Disease, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Bai Tao
- Department of Infectious Diseases, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Wuhan, Hubei, China
| | - Liwei Zhao
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Hang Xiao
- Yurogen Biosystem LLC, Wuhan, Hubei, China
| | - Xinyu Ding
- Department of Biological Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu, China
| | - Chuang Li
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Lin Chen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hao Cheng
- Yurogen Biosystem LLC, Wuhan, Hubei, China
| | - Yang Lou
- Yurogen Biosystem LLC, Wuhan, Hubei, China
| | - Yuxin Chen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- Institute of Viruses and Infectious Diseases, Nanjing University, Nanjing, Jiangsu, China
| | - Chao Wu
- Department of Infectious Diseases, Nanjing Drum Tower Hospital Clinical College of Xuzhou Medical University, Nanjing, Jiangsu, China
- Institute of Viruses and Infectious Diseases, Nanjing University, Nanjing, Jiangsu, China
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26
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Merling MR, Williams A, Mahfooz NS, Ruane-Foster M, Smith J, Jahnes J, Ayers LW, Bazan JA, Norris A, Norris Turner A, Oglesbee M, Faith SA, Quam MB, Robinson RT. The emergence of SARS-CoV-2 lineages and associated saliva antibody responses among asymptomatic individuals in a large university community. PLoS Pathog 2023; 19:e1011596. [PMID: 37603565 PMCID: PMC10470930 DOI: 10.1371/journal.ppat.1011596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 08/31/2023] [Accepted: 08/02/2023] [Indexed: 08/23/2023] Open
Abstract
SARS-CoV-2 (CoV2) infected, asymptomatic individuals are an important contributor to COVID transmission. CoV2-specific immunoglobulin (Ig)-as generated by the immune system following infection or vaccination-has helped limit CoV2 transmission from asymptomatic individuals to susceptible populations (e.g. elderly). Here, we describe the relationships between COVID incidence and CoV2 lineage, viral load, saliva Ig levels (CoV2-specific IgM, IgA and IgG), and ACE2 binding inhibition capacity in asymptomatic individuals between January 2021 and May 2022. These data were generated as part of a large university COVID monitoring program in Ohio, United States of America, and demonstrate that COVID incidence among asymptomatic individuals occurred in waves which mirrored those in surrounding regions, with saliva CoV2 viral loads becoming progressively higher in our community until vaccine mandates were established. Among the unvaccinated, infection with each CoV2 lineage (pre-Omicron) resulted in saliva Spike-specific IgM, IgA, and IgG responses, the latter increasing significantly post-infection and being more pronounced than N-specific IgG responses. Vaccination resulted in significantly higher Spike-specific IgG levels compared to unvaccinated infected individuals, and uninfected vaccinees' saliva was more capable of inhibiting Spike function. Vaccinees with breakthrough Delta infections had Spike-specific IgG levels comparable to those of uninfected vaccinees; however, their ability to inhibit Spike binding was diminished. These data are consistent with COVID vaccines having achieved hoped-for effects in our community, including the generation of mucosal antibodies that inhibit Spike and lower community viral loads, and suggest breakthrough Delta infections were not due to an absence of vaccine-elicited Ig, but instead limited Spike binding activity in the face of high community viral loads.
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Affiliation(s)
- Marlena R. Merling
- Department of Microbial Infection & Immunity, The Ohio State University, Columbus, Ohio, United States of America
| | - Amanda Williams
- Department of Microbial Infection & Immunity, The Ohio State University, Columbus, Ohio, United States of America
- Infectious Disease Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Najmus S. Mahfooz
- Department of Microbial Infection & Immunity, The Ohio State University, Columbus, Ohio, United States of America
| | - Marisa Ruane-Foster
- Department of Microbial Infection & Immunity, The Ohio State University, Columbus, Ohio, United States of America
| | - Jacob Smith
- Infectious Disease Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Jeff Jahnes
- Infectious Disease Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Leona W. Ayers
- Department of Pathology, The Ohio State University, Columbus, Ohio, United States of America
| | - Jose A. Bazan
- Division of Infectious Disease, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Alison Norris
- Division of Infectious Disease, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States of America
- Department of Epidemiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Abigail Norris Turner
- Division of Infectious Disease, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Michael Oglesbee
- Infectious Disease Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Seth A. Faith
- Infectious Disease Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Mikkel B. Quam
- Department of Epidemiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Richard T. Robinson
- Department of Microbial Infection & Immunity, The Ohio State University, Columbus, Ohio, United States of America
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27
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Fang L, Xu J, Zhao Y, Fan J, Shen J, Liu W, Cao G. The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2. Front Microbiol 2023; 14:1228128. [PMID: 37560529 PMCID: PMC10409611 DOI: 10.3389/fmicb.2023.1228128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/03/2023] [Indexed: 08/11/2023] Open
Abstract
Over three years' pandemic of 2019 novel coronavirus disease (COVID-19), multiple variants and novel subvariants have emerged successively, outcompeted earlier variants and become predominant. The sequential emergence of variants reflects the evolutionary process of mutation-selection-adaption of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Amino acid substitution/insertion/deletion in the spike protein causes altered viral antigenicity, transmissibility, and pathogenicity of SARS-CoV-2. Early in the pandemic, D614G mutation conferred virus with advantages over previous variants and increased transmissibility, and it also laid a conservative background for subsequent substantial mutations. The role of genomic recombination in the evolution of SARS-CoV-2 raised increasing concern with the occurrence of novel recombinants such as Deltacron, XBB.1.5, XBB.1.9.1, and XBB.1.16 in the late phase of pandemic. Co-circulation of different variants and co-infection in immunocompromised patients accelerate the emergence of recombinants. Surveillance for SARS-CoV-2 genomic variations, particularly spike protein mutation and recombination, is essential to identify ongoing changes in the viral genome and antigenic epitopes and thus leads to the development of new vaccine strategies and interventions.
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Affiliation(s)
- Letian Fang
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Jie Xu
- Department of Foreign Languages, International Exchange Center for Military Medicine, Second Military Medical University, Shanghai, China
| | - Yue Zhao
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Junyan Fan
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Jiaying Shen
- School of Medicine, Tongji University, Shanghai, China
| | - Wenbin Liu
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Guangwen Cao
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
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28
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Guo Y, Zhang G, Yang Q, Xie X, Lu Y, Cheng X, Wang H, Liang J, Tang J, Gao Y, Shang H, Dai J, Shi Y, Zhou J, Zhou J, Guo H, Yang H, Qi J, Liu L, Ma S, Zhang B, Huo Q, Xie Y, Wu J, Dong F, Zhang S, Lou Z, Gao Y, Song Z, Wang W, Sun Z, Yang X, Xiong D, Liu F, Chen X, Zhu P, Wang X, Cheng T, Rao Z. Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection. Nat Commun 2023; 14:3537. [PMID: 37322000 PMCID: PMC10267556 DOI: 10.1038/s41467-023-39267-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/30/2023] [Indexed: 06/17/2023] Open
Abstract
The SARS-CoV-2 Omicron variant evades most currently approved neutralizing antibodies (nAbs) and caused drastic decrease of plasma neutralizing activity elicited by vaccination or prior infection, urging the need for the development of pan-variant antivirals. Breakthrough infection induces a hybrid immunological response with potentially broad, potent and durable protection against variants, therefore, convalescent plasma from breakthrough infection may provide a broadened repertoire for identifying elite nAbs. We performed single-cell RNA sequencing (scRNA-seq) and BCR sequencing (scBCR-seq) of B cells from BA.1 breakthrough-infected patients who received 2 or 3 previous doses of inactivated vaccine. Elite nAbs, mainly derived from the IGHV2-5 and IGHV3-66/53 germlines, showed potent neutralizing activity across Wuhan-Hu-1, Delta, Omicron sublineages BA.1 and BA.2 at picomolar NT50 values. Cryo-EM analysis revealed diverse modes of spike recognition and guides the design of cocktail therapy. A single injection of paired antibodies cocktail provided potent protection in the K18-hACE2 transgenic female mouse model of SARS-CoV-2 infection.
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Grants
- National Natural Science Foundation of China (National Science Foundation of China)
- Chinese Academy of Medical Sciences (CAMS)
- This work was supported by the National Program on Key Research Project of China (2018YFE0200400, 2021YFE0201900, 2021YFA1100900 and 2018YFA0507200),The Key Program of Natural Science Foundation of Tianjin (20JCYBJC01340), Haihe Laboratory of Cell Ecosystem Innovation Fund (22HHXBSS00001),Science and Technology Project of Tianjin (22ZYJDSS00080),the Non-CAMS Fundamental Research Funds for Central Research Institutes (3332021093), Application for Basic and Applied Basic Research Projects of Guangzhou Basic Research Program (SL2023A04J00076), Emergency Key Program of Guangzhou Laboratory (EKPGL2021008), R&D Program of Guangzhou Laboratory (SRPG22-003, SRPG22-002).
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Affiliation(s)
- Yu Guo
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China.
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China.
- Beijing Institute of Biological Products Company Limited, China National Biotech Group, Beijing, 100176, China.
| | - Guangshun Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China
- Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China
- CNBG-Nankai Joint Research Center, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Frontiers Science Center for Cell Responses, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Qi Yang
- Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China.
| | - Xiaowei Xie
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Yang Lu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Xuelian Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Hui Wang
- Beijing Institute of Biological Products Company Limited, China National Biotech Group, Beijing, 100176, China
- CNBG-Nankai Joint Research Center, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Jingxi Liang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, P.R. China
| | - Jielin Tang
- Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China
| | - Yuxin Gao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China
- CNBG-Nankai Joint Research Center, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Frontiers Science Center for Cell Responses, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Hang Shang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China
- CNBG-Nankai Joint Research Center, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Frontiers Science Center for Cell Responses, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Jun Dai
- Guangzhou Customs District Technology Center, Guangzhou, 510700, China
| | - Yongxia Shi
- Guangzhou Customs District Technology Center, Guangzhou, 510700, China
| | - Jiaxi Zhou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Jun Zhou
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Hangtian Guo
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, P.R. China
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, P.R. China
| | - Jianwei Qi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Lijun Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Shihui Ma
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Biao Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Qianyu Huo
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Yi Xie
- Tianjin Haihe Hospital, Jingu Road, Tianjin, 300071, China
| | - Junping Wu
- Tianjin Haihe Hospital, Jingu Road, Tianjin, 300071, China
| | - Fang Dong
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China
- Frontiers Science Center for Cell Responses, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Song Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China
- Frontiers Science Center for Cell Responses, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Zhiyong Lou
- Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, P.R. China
| | - Zidan Song
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China
- Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China
- CNBG-Nankai Joint Research Center, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Frontiers Science Center for Cell Responses, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Wenming Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China
- CNBG-Nankai Joint Research Center, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Frontiers Science Center for Cell Responses, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Zixian Sun
- Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China
| | - Xiaoming Yang
- Beijing Institute of Biological Products Company Limited, China National Biotech Group, Beijing, 100176, China.
- CNBG-Nankai Joint Research Center, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
| | - Dongsheng Xiong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
| | - Fengjiang Liu
- Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China.
| | - Xinwen Chen
- Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China.
| | - Ping Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
| | - Ximo Wang
- Tianjin Haihe Hospital, Jingu Road, Tianjin, 300071, China.
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China.
- Guangzhou Laboratory, Guangzhou, Guangdong, People's Republic of China.
- CNBG-Nankai Joint Research Center, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, P.R. China.
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29
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Dimeglio C, Da-Silva I, Porcheron M, Panero MP, Staes L, Trémeaux P, Villars H, Izopet J. Weaker Effects of the Fourth Dose of BNT162b2 SARS-CoV-2 Vaccine on the Elderly Human Population. Vaccines (Basel) 2023; 11:1095. [PMID: 37376484 DOI: 10.3390/vaccines11061095] [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: 04/13/2023] [Revised: 06/03/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
The vaccines presently available are less effective in older people due to senescence of their immune systems. We measured the antibody responses of 42 adults living in nursing homes after the third and the fourth doses of an mRNA vaccine and found that the strain (BA.2 and BA.2.75: from 64 to 128, BA.5: from 16 to 32, BQ.1.1: from 16 to 64 among the uninfected) influenced the effect of the fourth dose of vaccine on neutralizing antibodies. The fourth dose also increased binding antibodies (from 1036 BAU/mL to 5371 BAU/mL among the uninfected, from 3700 BAU/mL to 6773 BAU/mL among the BA.5 infected). This effect was less significant than that of the third dose of vaccine for both neutralizing (BA.2: from 8 to 128, BA.5: from 2 to 16, BA.2.75: from 8 to 64, BQ.1.1: from 2 to 16) and binding antibodies (from 139.8 BAU/mL to 2293 BAU/mL). However, the fourth dose attained the 5000 BAU/mL threshold conferring approximately 80% protection against a SARS-CoV-2 BA.2 infection in most individuals, unlike the third.
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Affiliation(s)
- Chloé Dimeglio
- Virology Laboratory, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France
- Inserm UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), 31300 Toulouse, France
| | - Isabelle Da-Silva
- Virology Laboratory, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France
| | - Marion Porcheron
- Virology Laboratory, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France
| | | | - Laetitia Staes
- Virology Laboratory, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France
| | - Pauline Trémeaux
- Virology Laboratory, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France
- Inserm UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), 31300 Toulouse, France
| | - Hélène Villars
- Inserm UMR 1295: Center for Research in Population Health (CERPOP), Department of Epidemiology and Public Health, Toulouse, University of Toulouse III, 31073 Toulouse, France
- Geriatric Department, CHU Toulouse, Toulouse University Hospital, Hôpital Purpan Pavillon Leriche, 31300 Toulouse, France
| | - Jacques Izopet
- Virology Laboratory, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France
- Inserm UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), 31300 Toulouse, France
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30
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Rodriguez-Rodriguez BA, Ciabattoni GO, Duerr R, Valero-Jimenez AM, Yeung ST, Crosse KM, Schinlever AR, Bernard-Raichon L, Rodriguez Galvan J, McGrath ME, Vashee S, Xue Y, Loomis CA, Khanna KM, Cadwell K, Desvignes L, Frieman MB, Ortigoza MB, Dittmann M. A neonatal mouse model characterizes transmissibility of SARS-CoV-2 variants and reveals a role for ORF8. Nat Commun 2023; 14:3026. [PMID: 37230979 PMCID: PMC10211296 DOI: 10.1038/s41467-023-38783-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 05/15/2023] [Indexed: 05/27/2023] Open
Abstract
Small animal models have been a challenge for the study of SARS-CoV-2 transmission, with most investigators using golden hamsters or ferrets. Mice have the advantages of low cost, wide availability, less regulatory and husbandry challenges, and the existence of a versatile reagent and genetic toolbox. However, adult mice do not robustly transmit SARS-CoV-2. Here we establish a model based on neonatal mice that allows for transmission of clinical SARS-CoV-2 isolates. We characterize tropism, respiratory tract replication and transmission of ancestral WA-1 compared to variants Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), Omicron BA.1 and Omicron BQ.1.1. We identify inter-variant differences in timing and magnitude of infectious particle shedding from index mice, both of which shape transmission to contact mice. Furthermore, we characterize two recombinant SARS-CoV-2 lacking either the ORF6 or ORF8 host antagonists. The removal of ORF8 shifts viral replication towards the lower respiratory tract, resulting in significantly delayed and reduced transmission in our model. Our results demonstrate the potential of our neonatal mouse model to characterize viral and host determinants of SARS-CoV-2 transmission, while revealing a role for an accessory protein in this context.
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Affiliation(s)
| | - Grace O Ciabattoni
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Ralf Duerr
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Medicine/Division of Infectious Diseases and Immunology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Vaccine Center, NYU Grossmann of Medicine, New York, NY, 10016, USA
| | - Ana M Valero-Jimenez
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Stephen T Yeung
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Keaton M Crosse
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Austin R Schinlever
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Lucie Bernard-Raichon
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Joaquin Rodriguez Galvan
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Marisa E McGrath
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Sanjay Vashee
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD, 20850, USA
| | - Yong Xue
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD, 20850, USA
| | - Cynthia A Loomis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Kamal M Khanna
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, 10016, USA
| | - Ken Cadwell
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Ludovic Desvignes
- Department of Medicine/Division of Infectious Diseases and Immunology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- High Containment Laboratories - Office of Science and Research, NYU Langone Health, New York, NY, 10016, USA
| | - Matthew B Frieman
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Mila B Ortigoza
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
- Department of Medicine/Division of Infectious Diseases and Immunology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
| | - Meike Dittmann
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
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31
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Tamura T, Ito J, Uriu K, Zahradnik J, Kida I, Anraku Y, Nasser H, Shofa M, Oda Y, Lytras S, Nao N, Itakura Y, Deguchi S, Suzuki R, Wang L, Begum MM, Kita S, Yajima H, Sasaki J, Sasaki-Tabata K, Shimizu R, Tsuda M, Kosugi Y, Fujita S, Pan L, Sauter D, Yoshimatsu K, Suzuki S, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Yamamoto Y, Nagamoto T, Schreiber G, Maenaka K, Hashiguchi T, Ikeda T, Fukuhara T, Saito A, Tanaka S, Matsuno K, Takayama K, Sato K. Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants. Nat Commun 2023; 14:2800. [PMID: 37193706 DOI: 10.1038/s41467-023-38435-3] [Citation(s) in RCA: 86] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 05/02/2023] [Indexed: 05/18/2023] Open
Abstract
In late 2022, SARS-CoV-2 Omicron subvariants have become highly diversified, and XBB is spreading rapidly around the world. Our phylogenetic analyses suggested that XBB emerged through the recombination of two cocirculating BA.2 lineages, BJ.1 and BM.1.1.1 (a progeny of BA.2.75), during the summer of 2022. XBB.1 is the variant most profoundly resistant to BA.2/5 breakthrough infection sera to date and is more fusogenic than BA.2.75. The recombination breakpoint is located in the receptor-binding domain of spike, and each region of the recombinant spike confers immune evasion and increases fusogenicity. We further provide the structural basis for the interaction between XBB.1 spike and human ACE2. Finally, the intrinsic pathogenicity of XBB.1 in male hamsters is comparable to or even lower than that of BA.2.75. Our multiscale investigation provides evidence suggesting that XBB is the first observed SARS-CoV-2 variant to increase its fitness through recombination rather than substitutions.
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Affiliation(s)
- Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jiri Zahradnik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia
| | - Izumi Kida
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yuki Anraku
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
- Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Maya Shofa
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yoshitaka Oda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Spyros Lytras
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Naganori Nao
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Yukari Itakura
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan
| | - Lei Wang
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Mst Monira Begum
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Shunsuke Kita
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Hisano Yajima
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Jiei Sasaki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kaori Sasaki-Tabata
- Department of Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Ryo Shimizu
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Masumi Tsuda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Yusuke Kosugi
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shigeru Fujita
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Lin Pan
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Daniel Sauter
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | | | - Saori Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan
| | | | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | | | | | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Katsumi Maenaka
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo, Japan
- Division of Pathogen Structure, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
| | - Keita Matsuno
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan.
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
- One Health Research Center, Hokkaido University, Sapporo, Japan.
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan.
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan.
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.
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32
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Kaku CI, Starr TN, Zhou P, Dugan HL, Khalifé P, Song G, Champney ER, Mielcarz DW, Geoghegan JC, Burton DR, Andrabi R, Bloom JD, Walker LM. Evolution of antibody immunity following Omicron BA.1 breakthrough infection. Nat Commun 2023; 14:2751. [PMID: 37173311 PMCID: PMC10180619 DOI: 10.1038/s41467-023-38345-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Understanding the longitudinal dynamics of antibody immunity following heterologous SAR-CoV-2 breakthrough infection will inform the development of next-generation vaccines. Here, we track SARS-CoV-2 receptor binding domain (RBD)-specific antibody responses up to six months following Omicron BA.1 breakthrough infection in six mRNA-vaccinated individuals. Cross-reactive serum neutralizing antibody and memory B cell (MBC) responses decline by two- to four-fold through the study period. Breakthrough infection elicits minimal de novo Omicron BA.1-specific B cell responses but drives affinity maturation of pre-existing cross-reactive MBCs toward BA.1, which translates into enhanced breadth of activity across other variants. Public clones dominate the neutralizing antibody response at both early and late time points following breakthough infection, and their escape mutation profiles predict newly emergent Omicron sublineages, suggesting that convergent antibody responses continue to shape SARS-CoV-2 evolution. While the study is limited by our relatively small cohort size, these results suggest that heterologous SARS-CoV-2 variant exposure drives the evolution of B cell memory, supporting the continued development of next-generation variant-based vaccines.
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Affiliation(s)
- Chengzi I Kaku
- Adimab, LLC, Lebanon, NH, 03766, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Tyler N Starr
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Panpan Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | | | | | - Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | | | - Daniel W Mielcarz
- Dartmouth Cancer Center, Geisel School of Medicine, Lebanon, NH, 03766, USA
| | | | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, 02139, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98109, USA
- Howard Hughes Medical Institute, Seattle, WA, 98109, USA
| | - Laura M Walker
- Invivyd Inc., Waltham, MA, 02451, USA.
- Moderna, Inc., Cambridge, MA, USA.
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33
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Ito J, Suzuki R, Uriu K, Itakura Y, Zahradnik J, Kimura KT, Deguchi S, Wang L, Lytras S, Tamura T, Kida I, Nasser H, Shofa M, Begum MM, Tsuda M, Oda Y, Suzuki T, Sasaki J, Sasaki-Tabata K, Fujita S, Yoshimatsu K, Ito H, Nao N, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Yamamoto Y, Nagamoto T, Kuramochi J, Schreiber G, Saito A, Matsuno K, Takayama K, Hashiguchi T, Tanaka S, Fukuhara T, Ikeda T, Sato K. Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant. Nat Commun 2023; 14:2671. [PMID: 37169744 PMCID: PMC10175283 DOI: 10.1038/s41467-023-38188-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/18/2023] [Indexed: 05/13/2023] Open
Abstract
In late 2022, various Omicron subvariants emerged and cocirculated worldwide. These variants convergently acquired amino acid substitutions at critical residues in the spike protein, including residues R346, K444, L452, N460, and F486. Here, we characterize the convergent evolution of Omicron subvariants and the properties of one recent lineage of concern, BQ.1.1. Our phylogenetic analysis suggests that these five substitutions are recurrently acquired, particularly in younger Omicron lineages. Epidemic dynamics modelling suggests that the five substitutions increase viral fitness, and a large proportion of the fitness variation within Omicron lineages can be explained by these substitutions. Compared to BA.5, BQ.1.1 evades breakthrough BA.2 and BA.5 infection sera more efficiently, as demonstrated by neutralization assays. The pathogenicity of BQ.1.1 in hamsters is lower than that of BA.5. Our multiscale investigations illuminate the evolutionary rules governing the convergent evolution for known Omicron lineages as of 2022.
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Affiliation(s)
- Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yukari Itakura
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Jiri Zahradnik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia
| | - Kanako Terakado Kimura
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Lei Wang
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Spyros Lytras
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Izumi Kida
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
- Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Maya Shofa
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
| | - Mst Monira Begum
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Masumi Tsuda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Yoshitaka Oda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Tateki Suzuki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Jiei Sasaki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kaori Sasaki-Tabata
- Department of Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Shigeru Fujita
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | | | - Hayato Ito
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Naganori Nao
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development: HU-IVReD, Hokkaido University, Sapporo, Japan
| | | | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | | | | | - Jin Kuramochi
- Interpark Kuramochi Clinic, Utsunomiya, Japan
- Department of Global Health Promotion, Tokyo Medical and Dental University, Tokyo, Japan
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Keita Matsuno
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development: HU-IVReD, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
| | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan.
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan.
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan.
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Verkhivker G, Alshahrani M, Gupta G. Balancing Functional Tradeoffs between Protein Stability and ACE2 Binding in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB Lineages: Dynamics-Based Network Models Reveal Epistatic Effects Modulating Compensatory Dynamic and Energetic Changes. Viruses 2023; 15:1143. [PMID: 37243229 PMCID: PMC10221141 DOI: 10.3390/v15051143] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/27/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Evolutionary and functional studies suggested that the emergence of the Omicron variants can be determined by multiple fitness trade-offs including the immune escape, binding affinity for ACE2, conformational plasticity, protein stability and allosteric modulation. In this study, we systematically characterize conformational dynamics, structural stability and binding affinities of the SARS-CoV-2 Spike Omicron complexes with the host receptor ACE2 for BA.2, BA.2.75, XBB.1 and XBB.1.5 variants. We combined multiscale molecular simulations and dynamic analysis of allosteric interactions together with the ensemble-based mutational scanning of the protein residues and network modeling of epistatic interactions. This multifaceted computational study characterized molecular mechanisms and identified energetic hotspots that can mediate the predicted increased stability and the enhanced binding affinity of the BA.2.75 and XBB.1.5 complexes. The results suggested a mechanism driven by the stability hotspots and a spatially localized group of the Omicron binding affinity centers, while allowing for functionally beneficial neutral Omicron mutations in other binding interface positions. A network-based community model for the analysis of epistatic contributions in the Omicron complexes is proposed revealing the key role of the binding hotspots R498 and Y501 in mediating community-based epistatic couplings with other Omicron sites and allowing for compensatory dynamics and binding energetic changes. The results also showed that mutations in the convergent evolutionary hotspot F486 can modulate not only local interactions but also rewire the global network of local communities in this region allowing the F486P mutation to restore both the stability and binding affinity of the XBB.1.5 variant which may explain the growth advantages over the XBB.1 variant. The results of this study are consistent with a broad range of functional studies rationalizing functional roles of the Omicron mutation sites that form a coordinated network of hotspots enabling a balance of multiple fitness tradeoffs and shaping up a complex functional landscape of virus transmissibility.
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Affiliation(s)
- Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
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35
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Alboni S, Secco V, Papotti B, Vilella A, Adorni MP, Zimetti F, Schaeffer L, Tascedda F, Zoli M, Leblanc P, Villa E. Hydroxypropyl-β-Cyclodextrin Depletes Membrane Cholesterol and Inhibits SARS-CoV-2 Entry into HEK293T-ACE hi Cells. Pathogens 2023; 12:pathogens12050647. [PMID: 37242317 DOI: 10.3390/pathogens12050647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Vaccination has drastically decreased mortality due to coronavirus disease 19 (COVID-19), but not the rate of acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Alternative strategies such as inhibition of virus entry by interference with angiotensin-I-converting enzyme 2 (ACE2) receptors could be warranted. Cyclodextrins (CDs) are cyclic oligosaccharides that are able to deplete cholesterol from membrane lipid rafts, causing ACE2 receptors to relocate to areas devoid of lipid rafts. To explore the possibility of reducing SARS-CoV-2 entry, we tested hydroxypropyl-β-cyclodextrin (HPβCD) in a HEK293T-ACE2hi cell line stably overexpressing human ACE2 and Spike-pseudotyped SARS-CoV-2 lentiviral particles. We showed that HPβCD is not toxic to the cells at concentrations up to 5 mM, and that this concentration had no significant effect on cell cycle parameters in any experimental condition tested. Exposure of HEK293T-ACEhi cells to concentrations of HPβCD starting from 2.5 mM to 10 mM showed a concentration-dependent reduction of approximately 50% of the membrane cholesterol content. In addition, incubation of HEK293T-ACEhi cells with HIV-S-CoV-2 pseudotyped particles in the presence of increasing concentrations of HPβCD (from 0.1 to 10 mM) displayed a concentration-dependent effect on SARS-CoV-2 entry efficiency. Significant effects were detected at concentrations at least one order of magnitude lower than the lowest concentration showing toxic effects. These data indicate that HPβCD is a candidate for use as a SARS-CoV-2 prophylactic agent.
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Affiliation(s)
- Silvia Alboni
- Department of Life Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
- Centre for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Valentina Secco
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Bianca Papotti
- Department of Food and Drug, University of Parma, 43124 Parma, Italy
| | - Antonietta Vilella
- Centre for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, 41121 Modena, Italy
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Maria Pia Adorni
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy
| | - Francesca Zimetti
- Department of Food and Drug, University of Parma, 43124 Parma, Italy
| | - Laurent Schaeffer
- Institut NeuroMyoGène INMG-PGNM Pathophysiologie & Génétique du Neurone et du Muscle, UMR5261, Inserm U1315, 69008 Lyon, France
| | - Fabio Tascedda
- Department of Life Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
- Centre for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, 41121 Modena, Italy
- Consorzio Interuniversitario Biotecnologie (CIB), 34148 Trieste, Italy
| | - Michele Zoli
- Centre for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, 41121 Modena, Italy
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Pascal Leblanc
- Institut NeuroMyoGène INMG-PGNM Pathophysiologie & Génétique du Neurone et du Muscle, UMR5261, Inserm U1315, 69008 Lyon, France
| | - Erica Villa
- CHIMOMO Department, University of Modena and Reggio Emilia, and Azienda Ospedaliero-Universitaria di Modena, 41124 Modena, Italy
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36
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Faraone JN, Qu P, Evans JP, Zheng YM, Carlin C, Anghelina M, Stevens P, Fernandez S, Jones D, Lozanski G, Panchal A, Saif LJ, Oltz EM, Gumina RJ, Liu SL. Neutralization escape of Omicron XBB, BR.2, and BA.2.3.20 subvariants. Cell Rep Med 2023; 4:101049. [PMID: 37148877 DOI: 10.1016/j.xcrm.2023.101049] [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: 12/11/2022] [Revised: 01/17/2023] [Accepted: 04/20/2023] [Indexed: 05/08/2023]
Abstract
New Omicron subvariants continue to emerge throughout the world. In particular, the XBB subvariant, which is a recombinant virus between BA.2.10.1.1 and BA.2.75.3.1.1.1, as well as the BA.2.3.20 and BR.2 subvariants that contain mutations distinct from BA.2 and BA.2.75, are currently increasing in proportion of variants sequenced. Here we show that antibodies induced by 3-dose mRNA booster vaccination as well as BA.1- and BA.4/5-wave infection effectively neutralize BA.2, BR.2, and BA.2.3.20 but have significantly reduced efficiency against XBB. In addition, the BA.2.3.20 subvariant exhibits enhanced infectivity in the lung-derived CaLu-3 cells and in 293T-ACE2 cells. Overall, our results demonstrate that the XBB subvariant is highly neutralization resistant, which highlights the need for continued monitoring of the immune escape and tissue tropism of emerging Omicron subvariants.
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Affiliation(s)
- Julia N Faraone
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Panke Qu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - John P Evans
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Yi-Min Zheng
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Claire Carlin
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Mirela Anghelina
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Patrick Stevens
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Soledad Fernandez
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel Jones
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Gerard Lozanski
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Ashish Panchal
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Linda J Saif
- Center for Food Animal Health, Animal Sciences Department, OARDC, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; Veterinary Preventive Medicine Department, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA; Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Eugene M Oltz
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Richard J Gumina
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA; Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA.
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37
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Qu P, Faraone JN, Evans JP, Zheng YM, Carlin C, Anghelina M, Stevens P, Fernandez S, Jones D, Panchal AR, Saif LJ, Oltz EM, Zhang B, Zhou T, Xu K, Gumina RJ, Liu SL. Enhanced evasion of neutralizing antibody response by Omicron XBB.1.5, CH.1.1, and CA.3.1 variants. Cell Rep 2023; 42:112443. [PMID: 37104089 DOI: 10.1016/j.celrep.2023.112443] [Citation(s) in RCA: 59] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/04/2023] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
Omicron subvariants continuingly challenge current vaccination strategies. Here, we demonstrate nearly complete escape of the XBB.1.5, CH.1.1, and CA.3.1 variants from neutralizing antibodies stimulated by three doses of mRNA vaccine or by BA.4/5 wave infection, but neutralization is rescued by a BA.5-containing bivalent booster. CH.1.1 and CA.3.1 show strong immune escape from monoclonal antibody S309. Additionally, XBB.1.5, CH.1.1, and CA.3.1 spike proteins exhibit increased fusogenicity and enhanced processing compared with BA.2. Homology modeling reveals the key roles of G252V and F486P in the neutralization resistance of XBB.1.5, with F486P also enhancing receptor binding. Further, K444T/M and L452R in CH.1.1 and CA.3.1 likely drive escape from class II neutralizing antibodies, whereas R346T and G339H mutations could confer the strong neutralization resistance of these two subvariants to S309-like antibodies. Overall, our results support the need for administration of the bivalent mRNA vaccine and continued surveillance of Omicron subvariants.
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Affiliation(s)
- Panke Qu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Julia N Faraone
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - John P Evans
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Yi-Min Zheng
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Claire Carlin
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Mirela Anghelina
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Patrick Stevens
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Soledad Fernandez
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel Jones
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Ashish R Panchal
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Linda J Saif
- Center for Food Animal Health, Animal Sciences Department, OARDC, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; Veterinary Preventive Medicine Department, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA; Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Eugene M Oltz
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kai Xu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Richard J Gumina
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA; Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA.
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38
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Hersi F, Sebastian A, Tarazi H, Srinivasulu V, Mostafa A, Allayeh AK, Zeng C, Hachim IY, Liu SL, Abu-Yousef IA, Majdalawieh AF, Zaher DM, Omar HA, Al-Tel TH. Discovery of novel papain-like protease inhibitors for potential treatment of COVID-19. Eur J Med Chem 2023; 254:115380. [PMID: 37075625 PMCID: PMC10106510 DOI: 10.1016/j.ejmech.2023.115380] [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: 12/21/2022] [Revised: 03/09/2023] [Accepted: 04/12/2023] [Indexed: 04/21/2023]
Abstract
The recent emergence of different SARS-CoV-2 variants creates an urgent need to develop more effective therapeutic agents to prevent COVID-19 outbreaks. Among SARS-CoV-2 essential proteases is papain-like protease (SARS-CoV-2 PLpro), which plays multiple roles in regulating SARS-CoV-2 viral spread and innate immunity such as deubiquitinating and deISG15ylating (interferon-induced gene 15) activities. Many studies are currently focused on targeting this protease to tackle SARS-CoV-2 infection. In this context, we performed a phenotypic screening using an in-house pilot compounds collection possessing a diverse skeleta against SARS-CoV-2 PLpro. This screen identified SIMR3030 as a potent inhibitor of SARS-CoV-2. SIMR3030 has been shown to exhibit deubiquitinating activity and inhibition of SARS-CoV-2 specific gene expression (ORF1b and Spike) in infected host cells and possessing virucidal activity. Moreover, SIMR3030 was demonstrated to inhibit the expression of inflammatory markers, including IFN-α, IL-6, and OAS1, which are reported to mediate the development of cytokine storms and aggressive immune responses. In vitro absorption, distribution, metabolism, and excretion (ADME) assessment of the drug-likeness properties of SIMR3030 demonstrated good microsomal stability in liver microsomes. Furthermore, SIMR3030 demonstrated very low potency as an inhibitor of CYP450, CYP3A4, CYP2D6 and CYP2C9 which rules out any potential drug-drug interactions. In addition, SIMR3030 showed moderate permeability in Caco2-cells. Critically, SIMR3030 has maintained a high in vivo safety profile at different concentrations. Molecular modeling studies of SIMR3030 in the active sites of SARS-CoV-2 and MERS-CoV PLpro were performed to shed light on the binding modes of this inhibitor. This study demonstrates that SIMR3030 is a potent inhibitor of SARS-CoV-2 PLpro that forms the foundation for developing new drugs to tackle the COVID-19 pandemic and may pave the way for the development of novel therapeutics for a possible future outbreak of new SARS-CoV-2 variants or other Coronavirus species.
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Affiliation(s)
- Fatema Hersi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Anusha Sebastian
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Hamadeh Tarazi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Vunnam Srinivasulu
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, Environment and Climate Change Institute, National Research Centre, Giza, 12622, Egypt
| | - Abdou Kamal Allayeh
- Virology Lab 176, Water Pollution Research Department, Environment and Climate Change Institute, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Cong Zeng
- Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Ibrahim Y Hachim
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Imad A Abu-Yousef
- Department of Biology, Chemistry and Environmental Sciences, College of Arts and Sciences, American University of Sharjah, P.O. Box 26666, Sharjah, United Arab Emirates
| | - Amin F Majdalawieh
- Department of Biology, Chemistry and Environmental Sciences, College of Arts and Sciences, American University of Sharjah, P.O. Box 26666, Sharjah, United Arab Emirates
| | - Dana M Zaher
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Hany A Omar
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates; Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt.
| | - Taleb H Al-Tel
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates.
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Guo H, Yang Y, Zhao T, Lu Y, Gao Y, Li T, Xiao H, Chu X, Zheng L, Li W, Cheng H, Huang H, Liu Y, Lou Y, Nguyen HC, Wu C, Chen Y, Yang H, Ji X. Mechanism of a rabbit monoclonal antibody broadly neutralizing SARS-CoV-2 variants. Commun Biol 2023; 6:364. [PMID: 37012333 PMCID: PMC10069731 DOI: 10.1038/s42003-023-04759-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
Due to the continuous evolution of SARS-CoV-2, the Omicron variant has emerged and exhibits severe immune evasion. The high number of mutations at key antigenic sites on the spike protein has made a large number of existing antibodies and vaccines ineffective against this variant. Therefore, it is urgent to develop efficient broad-spectrum neutralizing therapeutic drugs. Here we characterize a rabbit monoclonal antibody (RmAb) 1H1 with broad-spectrum neutralizing potency against Omicron sublineages including BA.1, BA.1.1, BA.2, BA.2.12.1, BA.2.75, BA.3 and BA.4/5. Cryo-electron microscopy (cryo-EM) structure determination of the BA.1 spike-1H1 Fab complexes shows that 1H1 targets a highly conserved region of RBD and avoids most of the circulating Omicron mutations, explaining its broad-spectrum neutralization potency. Our findings indicate 1H1 as a promising RmAb model for designing broad-spectrum neutralizing antibodies and shed light on the development of therapeutic agents as well as effective vaccines against newly emerging variants in the future.
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Affiliation(s)
- Hangtian Guo
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Yixuan Yang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Tiantian Zhao
- Department of Infectious Diseases, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210008, China
| | - Yuchi Lu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China
| | - Tinghan Li
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Hang Xiao
- Yurogen Biosystem LLC, Wuhan, Hubei, 430075, China
| | - Xiaoyu Chu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Le Zheng
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Wanting Li
- Department of Infectious Diseases, Nanjing Drum Tower Hospital Clinical College of Xuzhou Medical University, Nanjing, Jiangsu, 210008, China
| | - Hao Cheng
- Yurogen Biosystem LLC, Wuhan, Hubei, 430075, China
| | - Haibin Huang
- Yurogen Biosystem LLC, Wuhan, Hubei, 430075, China
| | - Yang Liu
- Yurogen Biosystem LLC, Wuhan, Hubei, 430075, China
| | - Yang Lou
- Yurogen Biosystem LLC, Wuhan, Hubei, 430075, China
| | - Henry C Nguyen
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China
| | - Chao Wu
- Department of Infectious Diseases, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210008, China
- Institute of Viruses and Infectious Diseases, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Yuxin Chen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu, 210008, China.
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China
| | - Xiaoyun Ji
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China.
- Institute of Viruses and Infectious Diseases, Nanjing University, Nanjing, Jiangsu, 210008, China.
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu, 210008, China.
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Verkhivker G, Alshahrani M, Gupta G. Coarse-Grained Molecular Simulations and Ensemble-Based Mutational Profiling of Protein Stability in the Different Functional Forms of the SARS-CoV-2 Spike Trimers: Balancing Stability and Adaptability in BA.1, BA.2 and BA.2.75 Variants. Int J Mol Sci 2023; 24:ijms24076642. [PMID: 37047615 PMCID: PMC10094791 DOI: 10.3390/ijms24076642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
Evolutionary and functional studies have suggested that the emergence of Omicron variants can be determined by multiple fitness tradeoffs including immune escape, binding affinity, conformational plasticity, protein stability, and allosteric modulation. In this study, we embarked on a systematic comparative analysis of the conformational dynamics, electrostatics, protein stability, and allostery in the different functional states of spike trimers for BA.1, BA.2, and BA.2.75 variants. Using efficient and accurate coarse-grained simulations and atomistic reconstruction of the ensembles, we examined the conformational dynamics of the spike trimers that agree with the recent functional studies, suggesting that BA.2.75 trimers are the most stable among these variants. A systematic mutational scanning of the inter-protomer interfaces in the spike trimers revealed a group of conserved structural stability hotspots that play a key role in the modulation of functional dynamics and are also involved in the inter-protomer couplings through local contacts and interaction networks with the Omicron mutational sites. The results of mutational scanning provided evidence that BA.2.75 trimers are more stable than BA.2 and comparable in stability to the BA.1 variant. Using dynamic network modeling of the S Omicron BA.1, BA.2, and BA.2.75 trimers, we showed that the key network mediators of allosteric interactions are associated with the major stability hotspots that are interconnected along potential communication pathways. The network analysis of the BA.1, BA.2, and BA.2.75 trimers suggested that the increased thermodynamic stability of the BA.2.75 variant may be linked with the organization and modularity of the residue interaction network that allows for allosteric communications between structural stability hotspots and Omicron mutational sites. This study provided a plausible rationale for a mechanism in which Omicron mutations may evolve by targeting vulnerable sites of conformational adaptability to elicit immune escape while maintaining their control on balancing protein stability and functional fitness through robust allosteric communications with the stability hotspots.
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Affiliation(s)
- Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
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41
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Antibody response durability following three-dose coronavirus disease 2019 vaccination in people with HIV receiving suppressive antiretroviral therapy. AIDS 2023; 37:709-721. [PMID: 36545783 PMCID: PMC9994797 DOI: 10.1097/qad.0000000000003469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Limited data exist regarding longer term antibody responses following three-dose coronavirus disease 2019 (COVID-19) vaccination, and the impact of a first SARS-CoV-2 infection during this time, in people with HIV (PWH) receiving suppressive antiretroviral therapy (ART). We quantified wild-type-specific, Omicron BA.1-specific and Omicron BA.5-specific responses up to 6 months post-third dose in 64 PWH and 117 controls who remained COVID-19-naive or experienced their first SARS-CoV-2 infection during this time. DESIGN Longitudinal observational cohort. METHODS We quantified wild-type-specific and Omicron-specific anti-Spike receptor-binding domain IgG concentrations, ACE2 displacement activities and live virus neutralization at 1, 3 and 6 months post-third vaccine dose. RESULTS Third doses boosted all antibody measures above two-dose levels, but BA.1-specific responses remained significantly lower than wild-type-specific ones, with BA.5-specific responses lower still. Serum IgG concentrations declined at similar rates in COVID-19-naive PWH and controls post-third dose (median wild-type-specific and BA.1-specific half-lives were between 66 and 74 days for both groups). Antibody function also declined significantly yet comparably between groups: 6 months post-third dose, BA.1-specific neutralization was undetectable in more than 80% of COVID-19 naive PWH and more than 90% of controls. Breakthrough SARS-CoV-2 infection boosted antibody concentrations and function significantly above vaccine-induced levels in both PWH and controls, though BA.5-specific neutralization remained significantly poorer than BA.1 even post-breakthrough. CONCLUSION Following three-dose COVID-19 vaccination, antibody response durability in PWH receiving ART is comparable with controls. PWH also mounted strong responses to breakthrough infection. Due to temporal response declines, however, COVID-19-naive individuals, regardless of HIV status, would benefit from a fourth dose within 6 months of their third.
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Wang L, Møhlenberg M, Wang P, Zhou H. Immune evasion of neutralizing antibodies by SARS-CoV-2 Omicron. Cytokine Growth Factor Rev 2023; 70:13-25. [PMID: 36948931 PMCID: PMC9985919 DOI: 10.1016/j.cytogfr.2023.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/13/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023]
Abstract
Since its emergence at the end of 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the infection of more than 600 million people worldwide and has significant damage to global medical, economic, and political structures. Currently, a highly mutated variant of concern, SARS-CoV-2 Omicron, has evolved into many different subvariants mainly including BA.1, BA.2, BA.3, BA.4/5, and the recently emerging BA.2.75.2, BA.2.76, BA.4.6, BA.4.7, BA.5.9, BF.7, BQ.1, BQ.1.1, XBB, XBB.1, etc. Mutations in the N-terminal domain (NTD) of the spike protein, such as A67V, G142D, and N212I, alter the antigenic structure of Omicron, while mutations in the spike receptor binding domain (RBD), such as R346K, Q493R, and N501Y, increase the affinity for angiotensin-converting enzyme 2 (ACE2). Both types of mutations greatly increase the capacity of Omicron to evade immunity from neutralizing antibodies, produced by natural infection and/or vaccination. In this review, we systematically assess the immune evasion capacity of SARS-CoV-2, with an emphasis on the neutralizing antibodies generated by different vaccination regimes. Understanding the host antibody response and the evasion strategies employed by SARS-CoV-2 variants will improve our capacity to combat newly emerging Omicron variants.
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Affiliation(s)
- Lidong Wang
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | | | - Pengfei Wang
- State Key Laboratory of Genetic Engineering, Shanghai Institute of Infectious Disease and Biosecurity, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hao Zhou
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
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43
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Yang K, Wang C, Kreutzberger AJB, White KI, Pfuetzner RA, Esquivies L, Kirchhausen T, Brunger AT. Structure-based design of a SARS-CoV-2 Omicron-specific inhibitor. Proc Natl Acad Sci U S A 2023; 120:e2300360120. [PMID: 36940324 PMCID: PMC10068829 DOI: 10.1073/pnas.2300360120] [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: 01/07/2023] [Accepted: 02/13/2023] [Indexed: 03/22/2023] Open
Abstract
The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) introduced a relatively large number of mutations, including three mutations in the highly conserved heptad repeat 1 (HR1) region of the spike glycoprotein (S) critical for its membrane fusion activity. We show that one of these mutations, N969K induces a substantial displacement in the structure of the heptad repeat 2 (HR2) backbone in the HR1HR2 postfusion bundle. Due to this mutation, fusion-entry peptide inhibitors based on the Wuhan strain sequence are less efficacious. Here, we report an Omicron-specific peptide inhibitor designed based on the structure of the Omicron HR1HR2 postfusion bundle. Specifically, we inserted an additional residue in HR2 near the Omicron HR1 K969 residue to better accommodate the N969K mutation and relieve the distortion in the structure of the HR1HR2 postfusion bundle it introduced. The designed inhibitor recovers the loss of inhibition activity of the original longHR2_42 peptide with the Wuhan strain sequence against the Omicron variant in both a cell-cell fusion assay and a vesicular stomatitis virus (VSV)-SARS-CoV-2 chimera infection assay, suggesting that a similar approach could be used to combat future variants. From a mechanistic perspective, our work suggests the interactions in the extended region of HR2 may mediate the initial landing of HR2 onto HR1 during the transition of the S protein from the prehairpin intermediate to the postfusion state.
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Affiliation(s)
- Kailu Yang
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA94305
- Department of Structural Biology, Stanford University, Stanford, CA94305
- Department of Photon Science, Stanford University, Stanford, CA94305
| | - Chuchu Wang
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA94305
- Department of Structural Biology, Stanford University, Stanford, CA94305
- Department of Photon Science, Stanford University, Stanford, CA94305
| | - Alex J. B. Kreutzberger
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - K. Ian White
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA94305
- Department of Structural Biology, Stanford University, Stanford, CA94305
- Department of Photon Science, Stanford University, Stanford, CA94305
| | - Richard A. Pfuetzner
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA94305
- Department of Structural Biology, Stanford University, Stanford, CA94305
- Department of Photon Science, Stanford University, Stanford, CA94305
| | - Luis Esquivies
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA94305
- Department of Structural Biology, Stanford University, Stanford, CA94305
- Department of Photon Science, Stanford University, Stanford, CA94305
| | - Tomas Kirchhausen
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
| | - Axel T. Brunger
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA94305
- Department of Structural Biology, Stanford University, Stanford, CA94305
- Department of Photon Science, Stanford University, Stanford, CA94305
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44
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Qu P, Faraone JN, Evans JP, Zheng YM, Carlin C, Anghelina M, Stevens P, Fernandez S, Jones D, Panchal A, Saif LJ, Oltz EM, Xu K, Gumina RJ, Liu SL. Extraordinary Evasion of Neutralizing Antibody Response by Omicron XBB.1.5, CH.1.1 and CA.3.1 Variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.16.524244. [PMID: 36711991 PMCID: PMC9882202 DOI: 10.1101/2023.01.16.524244] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Newly emerging Omicron subvariants continue to emerge around the world, presenting potential challenges to current vaccination strategies. This study investigates the extent of neutralizing antibody escape by new subvariants XBB.1.5, CH.1.1, and CA.3.1, as well as their impacts on spike protein biology. Our results demonstrated a nearly complete escape of these variants from neutralizing antibodies stimulated by three doses of mRNA vaccine, but neutralization was rescued by a bivalent booster. However, CH.1.1 and CA.3.1 variants were highly resistant to both monovalent and bivalent mRNA vaccinations. We also assessed neutralization by sera from individuals infected during the BA.4/5 wave of infection and observed similar trends of immune escape. In these cohorts, XBB.1.5 did not exhibit enhanced neutralization resistance over the recently dominant BQ.1.1 variant. Notably, the spike proteins of XBB.1.5, CH.1.1, and CA.3.1 all exhibited increased fusogenicity compared to BA.2, correlating with enhanced S processing. Overall, our results support the administration of new bivalent mRNA vaccines, especially in fighting against newly emerged Omicron subvariants, as well as the need for continued surveillance of Omicron subvariants.
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Affiliation(s)
- Panke Qu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA,Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Julia N. Faraone
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA,Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA,Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - John P. Evans
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA,Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA,Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Yi-Min Zheng
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA,Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Claire Carlin
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Mirela Anghelina
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Patrick Stevens
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Soledad Fernandez
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Daniel Jones
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Ashish Panchal
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, USA
| | - Linda J. Saif
- Center for Food Animal Health, Animal Sciences Department, OARDC, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA,Veterinary Preventive Medicine Department, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA,Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Eugene M. Oltz
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Kai Xu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA,Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Richard J. Gumina
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA,Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA,Department of Physiology and Cell Biology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA,Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA,Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA,Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA,Corresponding Author:
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45
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Concern about the Effectiveness of mRNA Vaccination Technology and Its Long-Term Safety: Potential Interference on miRNA Machinery. Int J Mol Sci 2023; 24:ijms24021404. [PMID: 36674919 PMCID: PMC9863643 DOI: 10.3390/ijms24021404] [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: 11/22/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
After the outbreak of the pandemic due to COVID-19 infection, several vaccines were developed on short timelines to counteract the public health crisis. To allow the administration of mRNA vaccines through a faster-paced approval process, the Emergency Use Authorization (EUA) was applied. The Ba.5 (omicron) variant of SARS-CoV-2 is the predominant one at this moment. Its highly mutable single-stranded RNA genome, along with its high transmissivity, generated concern about the effectiveness of vaccination. The interaction between the vaccine and the host cell is finely regulated by miRNA machinery, a complex network that oversees a wide range of biological processes. The dysregulation of miRNA machinery has been associated with the development of clinical complications during COVID-19 infection and, moreover, to several human pathologies, among which is cancer disease. Now that in some areas, four doses of mRNA vaccine have been administered, it is natural to wonder about its effectiveness and long-term safety.
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46
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Widyasari K, Kim J. A Review of the Currently Available Antibody Therapy for the Treatment of Coronavirus Disease 2019 (COVID-19). Antibodies (Basel) 2023; 12:5. [PMID: 36648889 PMCID: PMC9887598 DOI: 10.3390/antib12010005] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/16/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Monoclonal antibodies are a promising treatment for COVID-19. However, the emergence of SARS-CoV-2 variants raised concerns about these therapies' efficacy and long-term viability. Studies reported several antibodies, that received authorization for COVID-19 treatment, are not effective against new variants or subvariants of SARS-CoV-2, hence their distribution has to be paused. Here, the authors reviewed the status of the currently available monoclonal antibodies for COVID-19 treatment, their potential as a therapeutic agent, and the challenges ahead. To address these issues, the authors presented general information on SARS-CoV-2 and how monoclonal antibodies work against SARS-CoV-2. The authors then focus on the antibodies that have been deployed for COVID-19 treatment and their current status, as well as the evidence supporting their potential as an early intervention against COVID-19. Lastly, the authors discussed some leading obstacles that hinder the development and administration of monoclonal antibodies for the treatment of COVID-19.
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Affiliation(s)
- Kristin Widyasari
- Gyeongsang Institute of Health Sciences, Gyeongsang National University, Jinju 52727, Republic of Korea
| | - Jinnam Kim
- Major of Food Science & Nutrition, Pukyong National University, Busan 48513, Republic of Korea
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47
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Qu P, Evans JP, Faraone JN, Zheng YM, Carlin C, Anghelina M, Stevens P, Fernandez S, Jones D, Lozanski G, Panchal A, Saif LJ, Oltz EM, Xu K, Gumina RJ, Liu SL. Enhanced neutralization resistance of SARS-CoV-2 Omicron subvariants BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2. Cell Host Microbe 2023; 31:9-17.e3. [PMID: 36476380 PMCID: PMC9678813 DOI: 10.1016/j.chom.2022.11.012] [Citation(s) in RCA: 124] [Impact Index Per Article: 124.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/10/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022]
Abstract
The continued evolution of SARS-CoV-2 has led to the emergence of several new Omicron subvariants, including BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2. Here, we examine the neutralization resistance of these subvariants against sera from 3-dose vaccinated healthcare workers, hospitalized BA.1-wave patients, and BA.4/5-wave patients. We found enhanced neutralization resistance in all new subvariants, especially in the BQ.1 and BQ.1.1 subvariants driven by N460K and K444T mutations, as well as the BA.2.75.2 subvariant driven largely by its F486S mutation. All Omicron subvariants maintained their weakened infectivity in Calu-3 cells, with the F486S mutation driving further diminished titer for the BA.2.75.2 subvariant. Molecular modeling revealed the mechanisms of antibody-mediated immune evasion by R346T, K444T, F486S, and D1199N mutations. Altogether, these findings shed light on the evolution of newly emerging SARS-CoV-2 Omicron subvariants.
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Affiliation(s)
- Panke Qu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA,Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - John P. Evans
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA,Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA,Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Julia N. Faraone
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA,Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA,Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Yi-Min Zheng
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA,Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Claire Carlin
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Mirela Anghelina
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Patrick Stevens
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Soledad Fernandez
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel Jones
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Gerard Lozanski
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Ashish Panchal
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Linda J. Saif
- Center for Food Animal Health, Animal Sciences Department, OARDC, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA,Veterinary Preventive Medicine Department, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA,Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Eugene M. Oltz
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Kai Xu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA,Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Richard J. Gumina
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA,Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA,Department of Physiology and Cell Biology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA,Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA,Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA,Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA,Corresponding author
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48
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Muacevic A, Adler JR. Attenuation and Degeneration of SARS-CoV-2 Despite Adaptive Evolution. Cureus 2023; 15:e33316. [PMID: 36741655 PMCID: PMC9894646 DOI: 10.7759/cureus.33316] [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: 11/17/2022] [Accepted: 01/02/2023] [Indexed: 01/04/2023] Open
Abstract
The evolution of severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) has followed similar trends as other RNA viruses, such as human immunodeficiency virus type 1 and the influenza A virus. Rapid initial diversification was followed by strong competition and a rapid succession of dominant variants. Host-initiated RNA editing has been the primary mechanism for introducing mutations. A significant number of mutations detrimental to viral replication have been quickly purged. Fixed mutations are mostly diversifying mutations selected for host adaptation and immune evasion, with the latter accounting for the majority of the mutations. However, immune evasion often comes at the cost of functionality, and thus, optimal functionality is still far from being accomplished. Instead, selection for antibody-escaping variants and accumulation of near-neutral mutations have led to suboptimal codon usage and reduced replicative capacity, as demonstrated in non-respiratory cell lines. Beneficial adaptation of the virus includes reduced infectivity in lung tissues and increased tropism for the upper airway, resulting in shorter incubation periods, milder diseases, and more efficient transmission between people.
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49
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Xiang T, Wang J, Zheng X. The humoral and cellular immune evasion of SARS-CoV-2 Omicron and sub-lineages. Virol Sin 2022; 37:786-795. [PMID: 36427646 PMCID: PMC9681989 DOI: 10.1016/j.virs.2022.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
The recently discovered SARS-CoV-2 variant Omicron (B.1.1.529) has rapidly become a global public health issue. The substantial mutations in the spike protein in this new variant have raised concerns about its ability to escape from pre-existing immunity established by natural infection or vaccination. In this review, we give a summary of current knowledge concerning the antibody evasion properties of Omicron and its subvariants (BA.2, BA.2.12.1, BA.4/5, and BA.2.75) from therapeutic monoclonal antibodies and the sera of SARS-CoV-2 vaccine recipients or convalescent patients. We also summarize whether vaccine-induced cellular immunity (memory B cell and T cell response) can recognize Omicron specifically. In brief, the Omicron variants demonstrated remarkable antibody evasion, with even more striking antibody escape seen in the Omicron BA.4 and BA.5 sub-lineages. Luckily, the third booster vaccine dose significantly increased the neutralizing antibodies titers, and the vaccine-induced cellular response remains conserved and provides second-line defense against the Omicron.
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Affiliation(s)
- Tiandan Xiang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Junzhong Wang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Xin Zheng
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan 430022, China.
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50
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Qu P, Evans JP, Faraone JN, Zheng YM, Carlin C, Anghelina M, Stevens P, Fernandez S, Jones D, Lozanski G, Panchal A, Saif LJ, Oltz EM, Xu K, Gumina RJ, Liu SL. Enhanced neutralization resistance of SARS-CoV-2 Omicron subvariants BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2. Cell Host Microbe 2022. [PMID: 36476380 DOI: 10.1101/2022.10.19.512891v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The continued evolution of SARS-CoV-2 has led to the emergence of several new Omicron subvariants, including BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2. Here, we examine the neutralization resistance of these subvariants against sera from 3-dose vaccinated healthcare workers, hospitalized BA.1-wave patients, and BA.4/5-wave patients. We found enhanced neutralization resistance in all new subvariants, especially in the BQ.1 and BQ.1.1 subvariants driven by N460K and K444T mutations, as well as the BA.2.75.2 subvariant driven largely by its F486S mutation. All Omicron subvariants maintained their weakened infectivity in Calu-3 cells, with the F486S mutation driving further diminished titer for the BA.2.75.2 subvariant. Molecular modeling revealed the mechanisms of antibody-mediated immune evasion by R346T, K444T, F486S, and D1199N mutations. Altogether, these findings shed light on the evolution of newly emerging SARS-CoV-2 Omicron subvariants.
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Affiliation(s)
- Panke Qu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - John P Evans
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Julia N Faraone
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Yi-Min Zheng
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Claire Carlin
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Mirela Anghelina
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Patrick Stevens
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Soledad Fernandez
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel Jones
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Gerard Lozanski
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Ashish Panchal
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Linda J Saif
- Center for Food Animal Health, Animal Sciences Department, OARDC, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; Veterinary Preventive Medicine Department, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA; Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Eugene M Oltz
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Kai Xu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Richard J Gumina
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA; Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA.
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