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De Greve H, Fioravanti A. Single domain antibodies from camelids in the treatment of microbial infections. Front Immunol 2024; 15:1334829. [PMID: 38827746 PMCID: PMC11140111 DOI: 10.3389/fimmu.2024.1334829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/29/2024] [Indexed: 06/04/2024] Open
Abstract
Infectious diseases continue to pose significant global health challenges. In addition to the enduring burdens of ailments like malaria and HIV, the emergence of nosocomial outbreaks driven by antibiotic-resistant pathogens underscores the ongoing threats. Furthermore, recent infectious disease crises, exemplified by the Ebola and SARS-CoV-2 outbreaks, have intensified the pursuit of more effective and efficient diagnostic and therapeutic solutions. Among the promising options, antibodies have garnered significant attention due to their favorable structural characteristics and versatile applications. Notably, nanobodies (Nbs), the smallest functional single-domain antibodies of heavy-chain only antibodies produced by camelids, exhibit remarkable capabilities in stable antigen binding. They offer unique advantages such as ease of expression and modification and enhanced stability, as well as improved hydrophilicity compared to conventional antibody fragments (antigen-binding fragments (Fab) or single-chain variable fragments (scFv)) that can aggregate due to their low solubility. Nanobodies directly target antigen epitopes or can be engineered into multivalent Nbs and Nb-fusion proteins, expanding their therapeutic potential. This review is dedicated to charting the progress in Nb research, particularly those derived from camelids, and highlighting their diverse applications in treating infectious diseases, spanning both human and animal contexts.
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Affiliation(s)
- Henri De Greve
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Antonella Fioravanti
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
- Fondazione ParSeC – Parco delle Scienze e della Cultura, Prato, Italy
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2
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Sultana N, Nagesha SN, Reddy CNL, Ramesh BN, Shyamalamma S, Shashidhara KS, Satish KM, Pradeep C, Vidyadhar GD. Computational analysis of affinity dynamics between the variants of SARS-CoV-2 spike protein (RBD) and human ACE-2 receptor. Virol J 2024; 21:88. [PMID: 38641844 PMCID: PMC11031966 DOI: 10.1186/s12985-024-02365-3] [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: 03/20/2024] [Accepted: 04/13/2024] [Indexed: 04/21/2024] Open
Abstract
The novel coronavirus SARS-CoV-2 resulted in a significant worldwide health emergency known as the COVID-19 pandemic. This crisis has been marked by the widespread of various variants, with certain ones causing notable apprehension. In this study, we harnessed computational techniques to scrutinize these Variants of Concern (VOCs), including various Omicron subvariants. Our approach involved the use of protein structure prediction algorithms and molecular docking techniques, we have investigated the effects of mutations within the Receptor Binding Domain (RBD) of SARS-CoV-2 and how these mutations influence its interactions with the human angiotensin-converting enzyme 2 (hACE-2) receptor. Further we have predicted the structural alterations in the RBD of naturally occurring SARS-CoV-2 variants using the tr-Rosetta algorithm. Subsequent docking and binding analysis employing HADDOCK and PRODIGY illuminated crucial interactions occurring at the Receptor-Binding Motif (RBM). Our findings revealed a hierarchy of increased binding affinity between the human ACE2 receptor and the various RBDs, in the order of wild type (Wuhan-strain) < Beta < Alpha < Gamma < Omicron-B.1.1.529 < Delta < Omicron-BA.2.12.1 < Omicron-BA.5.2.1 < Omicron-BA.1.1. Notably, Omicron-BA.1.1 demonstrated the highest binding affinity of -17.4 kcal mol-1 to the hACE2 receptor when compared to all the mutant complexes. Additionally, our examination indicated that mutations occurring in active residues of the Receptor Binding Domain (RBD) consistently improved the binding affinity and intermolecular interactions in all mutant complexes. Analysis of the differences among variants has laid a foundation for the structure-based drug design targeting the RBD region of SARS-CoV-2.
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Affiliation(s)
- Nishad Sultana
- Department of Plant Biotechnology, University of Agricultural Sciences, GKVK, Bangalore, 560 065, India
| | - S N Nagesha
- Department of Plant Biotechnology, College of Agriculture, Hassan, UAS, Bangalore, 573 225, India.
| | | | - B N Ramesh
- ICAR-PHT, UAS, GKVK, Bangalore, 560 065, India
| | - S Shyamalamma
- Department of Plant Biotechnology, University of Agricultural Sciences, GKVK, Bangalore, 560 065, India
| | - K S Shashidhara
- Department of Genetics and Plant Breeding, College of Agriculture, Hassan, UAS, Bangalore, 573 225, India
| | - K M Satish
- Department Biotechnology, KSNUAHS, Shivamogga, 577 412, India
| | - C Pradeep
- Department of Plant Biotechnology, University of Agricultural Sciences, GKVK, Bangalore, 560 065, India
| | - G D Vidyadhar
- Department of Plant Biotechnology, University of Agricultural Sciences, GKVK, Bangalore, 560 065, India
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Kumar A, Vashisth H. Quantitative Assessment of Energetic Contributions of Residues in a SARS-CoV-2 Viral Enzyme/Nanobody Interface. J Chem Inf Model 2024; 64:2068-2076. [PMID: 38460144 DOI: 10.1021/acs.jcim.3c01933] [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] [Indexed: 03/11/2024]
Abstract
The highly conserved protease enzyme from SARS-CoV-2 (MPro) is crucial for viral replication and is an attractive target for the design of novel inhibitory compounds. MPro is known to be conformationally flexible and has been stabilized in an extended conformation in a complex with a novel nanobody (NB2B4), which inhibits the dimerization of the enzyme via binding to an allosteric site. However, the energetic contributions of the nanobody residues stabilizing the MPro/nanobody interface remain unresolved. We probed these residues using all-atom MD simulations in combination with alchemical free energy calculations by studying the physical residue-residue interactions and discovered the role of hydrophobic and electrostatic interactions in stabilizing the complex. Specifically, we found via mutational analysis that three interfacial nanobody residues (Y59, R106, and L109) contributed significantly, two residues (L107 and P110) contributed moderately, and two residues (H112 and T113) contributed minimally to the overall binding affinity of the nanobody. We also discovered that the nanobody affinity could be enhanced via a charge-reversal mutation (D62R) that alters the local interfacial electrostatic environment of this residue in the complex. These findings are potentially useful in designing novel synthetic nanobodies as allosteric inhibitors of MPro.
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Affiliation(s)
- Amit Kumar
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
| | - Harish Vashisth
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, New Hampshire 03824, United States
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4
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Jabeen M, Shoukat S, Shireen H, Bao Y, Khan A, Abbasi AA. Unraveling the genetic variations underlying virulence disparities among SARS-CoV-2 strains across global regions: insights from Pakistan. Virol J 2024; 21:55. [PMID: 38449001 PMCID: PMC10916261 DOI: 10.1186/s12985-024-02328-8] [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: 09/23/2023] [Accepted: 02/26/2024] [Indexed: 03/08/2024] Open
Abstract
Over the course of the COVID-19 pandemic, several SARS-CoV-2 variants have emerged that may exhibit different etiological effects such as enhanced transmissibility and infectivity. However, genetic variations that reduce virulence and deteriorate viral fitness have not yet been thoroughly investigated. The present study sought to evaluate the effects of viral genetic makeup on COVID-19 epidemiology in Pakistan, where the infectivity and mortality rate was comparatively lower than other countries during the first pandemic wave. For this purpose, we focused on the comparative analyses of 7096 amino-acid long polyprotein pp1ab. Comparative sequence analysis of 203 SARS-CoV-2 genomes, sampled from Pakistan during the first wave of the pandemic revealed 179 amino acid substitutions in pp1ab. Within this set, 38 substitutions were identified within the Nsp3 region of the pp1ab polyprotein. Structural and biophysical analysis of proteins revealed that amino acid variations within Nsp3's macrodomains induced conformational changes and modified protein-ligand interactions, consequently diminishing the virulence and fitness of SARS-CoV-2. Additionally, the epistatic effects resulting from evolutionary substitutions in SARS-CoV-2 proteins may have unnoticed implications for reducing disease burden. In light of these findings, further characterization of such deleterious SARS-CoV-2 mutations will not only aid in identifying potential therapeutic targets but will also provide a roadmap for maintaining vigilance against the genetic variability of diverse SARS-CoV-2 strains circulating globally. Furthermore, these insights empower us to more effectively manage and respond to potential viral-based pandemic outbreaks of a similar nature in the future.
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Affiliation(s)
- Momina Jabeen
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad, Pakistan
| | - Shifa Shoukat
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad, Pakistan
| | - Huma Shireen
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad, Pakistan
| | - Yiming Bao
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
- School of Medical and Life Sciences, Sunway University, Sunway City, Malaysia
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad, Pakistan.
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Carossino M, Izadmehr S, Trujillo JD, Gaudreault NN, Dittmar W, Morozov I, Balasuriya UBR, Cordon-Cardo C, García-Sastre A, Richt JA. ACE2 and TMPRSS2 distribution in the respiratory tract of different animal species and its correlation with SARS-CoV-2 tissue tropism. Microbiol Spectr 2024; 12:e0327023. [PMID: 38230954 PMCID: PMC10846196 DOI: 10.1128/spectrum.03270-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/08/2023] [Indexed: 01/18/2024] Open
Abstract
A wide range of animal species show variable susceptibility to SARS-CoV-2; however, host factors associated with varied susceptibility remain to be defined. Here, we examined whether susceptibility to SARS-CoV-2 and virus tropism in different animal species are dependent on the expression and distribution of the virus receptor angiotensin-converting enzyme 2 (ACE2) and the host cell factor transmembrane serine protease 2 (TMPRSS2). We cataloged the upper and lower respiratory tract of multiple animal species and humans in a tissue-specific manner and quantitatively evaluated the distribution and abundance of ACE2 and TMPRSS2 mRNA in situ. Our results show that: (i) ACE2 and TMPRSS2 mRNA are abundant in the conduction portion of the respiratory tract, (ii) ACE2 mRNA occurs at a lower abundance compared to TMPRSS2 mRNA, (iii) co-expression of ACE2-TMPRSS2 mRNAs is highest in those species with the highest susceptibility to SARS-CoV-2 infection (i.e., cats, Syrian hamsters, and white-tailed deer), and (iv) expression of ACE2 and TMPRSS2 mRNA was not altered following SARS-CoV-2 infection. Our results demonstrate that while specific regions of the respiratory tract are enriched in ACE2 and TMPRSS2 mRNAs in different animal species, this is only a partial determinant of susceptibility to SARS-CoV-2 infection.IMPORTANCESARS-CoV-2 infects a wide array of domestic and wild animals, raising concerns regarding its evolutionary dynamics in animals and potential for spillback transmission of emerging variants to humans. Hence, SARS-CoV-2 infection in animals has significant public health relevance. Host factors determining animal susceptibility to SARS-CoV-2 are vastly unknown, and their characterization is critical to further understand susceptibility and viral dynamics in animal populations and anticipate potential spillback transmission. Here, we quantitatively assessed the distribution and abundance of the two most important host factors, angiotensin-converting enzyme 2 and transmembrane serine protease 2, in the respiratory tract of various animal species and humans. Our results demonstrate that while specific regions of the respiratory tract are enriched in these two host factors, they are only partial determinants of susceptibility. Detailed analysis of additional host factors is critical for our understanding of the underlying mechanisms governing viral susceptibility and reservoir hosts.
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Affiliation(s)
- Mariano Carossino
- Department of Pathobiological Sciences and Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Sudeh Izadmehr
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jessie D. Trujillo
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Wellesley Dittmar
- Department of Pathobiological Sciences and Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Igor Morozov
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Udeni B. R. Balasuriya
- Department of Pathobiological Sciences and Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adolfo García-Sastre
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
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Xie L, Shi S, Cheng L, Xu B, Ma S, Liu J, Wu X, Wang Y, Ye S. Dauricine interferes with SARS-CoV-2 variants infection by blocking the interface between RBD and ACE2. Int J Biol Macromol 2023; 253:127344. [PMID: 37848107 DOI: 10.1016/j.ijbiomac.2023.127344] [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: 09/08/2023] [Revised: 10/07/2023] [Accepted: 10/08/2023] [Indexed: 10/19/2023]
Abstract
The continued viral evolution results in the emergence of various SARS-CoV-2 variants, such as delta or omicron, that are partially resistant to current vaccines and antiviral medicines, posing an increased risk to global public health and raising the importance of continuous development of antiviral medicines. Inhibitor screening targeting the interactions between the viral spike proteins and their human receptor ACE2 represents a promising approach for drug discovery. Here, we demonstrate that the evolutionary trend of the SARS-CoV-2 variants is associated with increased electrostatic interactions between S proteins and ACE2. Virtual screening based on the ACE2-RBD binding interface identified nine monomers of Traditional Chinese medicine (TCM). Furthermore, live-virus neutralization assays revealed that Dauricine, one of the identified monomers, exhibited an antiviral activity with an IC50 range of 18.2 to 33.3 μM for original strain, Delta, and Omicron strains, respectively. The computational study showed that the polycyclic and methoxy groups of Dauricine adhere to the RBD surface through π-π and electrostatic interactions. The discovery of Dauricine is a successful attempt to target viral entry, which will not only help society to respond quickly to viral variants, but also accelerate variant drug development thereby reducing the pressure on health authorities to respond to outbreaks.
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Affiliation(s)
- Lei Xie
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Sai Shi
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Lin Cheng
- Institute for Hepatology, Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Binghong Xu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Sen Ma
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Jie Liu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Xilin Wu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, 210023, China.
| | - Yaxin Wang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China.
| | - Sheng Ye
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China.
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7
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Holdenrieder S, Dos Santos Ferreira CE, Izopet J, Theel ES, Wieser A. Clinical and laboratory considerations: determining an antibody-based composite correlate of risk for reinfection with SARS-CoV-2 or severe COVID-19. Front Public Health 2023; 11:1290402. [PMID: 38222091 PMCID: PMC10788057 DOI: 10.3389/fpubh.2023.1290402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/30/2023] [Indexed: 01/16/2024] Open
Abstract
Much of the global population now has some level of adaptive immunity to SARS-CoV-2 induced by exposure to the virus (natural infection), vaccination, or a combination of both (hybrid immunity). Key questions that subsequently arise relate to the duration and the level of protection an individual might expect based on their infection and vaccination history. A multi-component composite correlate of risk (CoR) could inform individuals and stakeholders about protection and aid decision making. This perspective evaluates the various elements that need to be accommodated in the development of an antibody-based composite CoR for reinfection with SARS-CoV-2 or development of severe COVID-19, including variation in exposure dose, transmission route, viral genetic variation, patient factors, and vaccination status. We provide an overview of antibody dynamics to aid exploration of the specifics of SARS-CoV-2 antibody testing. We further discuss anti-SARS-CoV-2 immunoassays, sample matrices, testing formats, frequency of sampling and the optimal time point for such sampling. While the development of a composite CoR is challenging, we provide our recommendations for each of these key areas and highlight areas that require further work to be undertaken.
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Affiliation(s)
- Stefan Holdenrieder
- Institute of Laboratory Medicine, German Heart Centre Munich, Technical University Munich, Munich, Germany
| | | | - Jacques Izopet
- Laboratory of Virology, Toulouse University Hospital and INFINITY Toulouse Institute for Infections and Inflammatory Diseases, INSERM UMR 1291 CNRS UMR 5051, University Toulouse III, Toulouse, France
| | - Elitza S. Theel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Centre for Infection Research (DZIF), Munich, Germany
- Faculty of Medicine, Max Von Pettenkofer Institute, LMU Munich, Munich, Germany
- Immunology, Infection and Pandemic Research, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Munich, Germany
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Ashraf J, Bukhari SARS, Kanji A, Iqbal T, Yameen M, Nisar MI, Khan W, Hasan Z. Substitution spectra of SARS-CoV-2 genome from Pakistan reveals insights into the evolution of variants across the pandemic. Sci Rep 2023; 13:20955. [PMID: 38017265 PMCID: PMC10684861 DOI: 10.1038/s41598-023-48272-5] [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: 07/09/2023] [Accepted: 11/24/2023] [Indexed: 11/30/2023] Open
Abstract
Changing morbidity and mortality due to COVID-19 across the pandemic has been linked with factors such as the emergence of SARS-CoV-2 variants and vaccination. Mutations in the Spike glycoprotein enhanced viral transmission and virulence. We investigated whether SARS-CoV-2 mutation rates and entropy were associated COVID-19 in Pakistan, before and after the introduction of vaccinations. We analyzed 1,705 SARS-CoV-2 genomes using the Augur phylogenetic pipeline. Substitution rates and entropy across the genome, and in the Spike glycoprotein were compared between 2020, 2021 and 2022 (as periods A, B and C). Mortality was greatest in B whilst cases were highest during C. In period A, G clades were predominant, and substitution rate was 5.25 × 10-4 per site per year. In B, Delta variants dominated, and substitution rates increased to 9.74 × 10-4. In C, Omicron variants led to substitution rates of 5.02 × 10-4. Genome-wide entropy was the highest during B particularly, at Spike E484K and K417N. During C, genome-wide mutations increased whilst entropy was reduced. Enhanced SARS-CoV-2 genome substitution rates were associated with a period when more virulent SARS-CoV-2 variants were prevalent. Reduced substitution rates and stabilization of genome entropy was subsequently evident when vaccinations were introduced. Whole genome entropy analysis can help predict virus evolution to guide public health interventions.
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Affiliation(s)
- Javaria Ashraf
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan
| | - Sayed Ali Raza Shah Bukhari
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan
| | - Akbar Kanji
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan
| | - Tulaib Iqbal
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan
| | - Maliha Yameen
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan
| | - Muhammad Imran Nisar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
- Department of Pediatrics and Child Health, CITRIC Center for Bioinformatics and Computational Biology, Aga Khan University, Karachi, Pakistan
| | - Waqasuddin Khan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
- Department of Pediatrics and Child Health, CITRIC Center for Bioinformatics and Computational Biology, Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan.
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9
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Prasad R, Ajith H, Kumar Chandrakumaran N, Dnyaneshwar Khangar P, Mohan A, Nelson-Sathi S. In silico study identifies peptide inhibitors that negate the effect of non-synonymous mutations in major drug targets of SARS-CoV-2 variants. J Biomol Struct Dyn 2023; 41:9551-9561. [PMID: 36377464 DOI: 10.1080/07391102.2022.2143426] [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: 09/15/2022] [Accepted: 10/29/2022] [Indexed: 11/16/2022]
Abstract
Since its advent in December 2019, SARS-CoV-2 has diverged into multiple variants with differing levels of virulence owing to the accumulation of mutations in its genome. The structural changes induced by non-synonymous mutations in major drug targets of the virus are known to alter the binding of potential antagonistic inhibitors. Here, we analyzed the effects of non-synonymous mutations in major targets of SARS-CoV-2 in response to potential peptide inhibitors. We screened 12 peptides reported to have anti-viral properties against RBD and 5 peptides against Mpro of SARS-CoV-2 variants using molecular docking and simulation approaches. The mutational landscape of RBD among SARS-CoV-2 variants had 21 non-synonymous mutations across 18 distinct sites. Among these, 14 mutations were present in the RBM region directly interacting with the hACE2 receptor. However, Only 3 non-synonymous mutations were observed in Mpro. We found that LCB1 - a de novo-synthesized peptide has the highest binding affinity to RBD despite non-synonymous mutations in variants and engages key residues of RBD-hACE2 interaction such as K417, E484, N487, and N501. Similarly, an antimicrobial peptide; 2JOS, was identified against Mpro with high binding affinity as it interacts with key residues in dimerization sites such as E166 and F140 crucial for viral replication. MD simulations affirm the stability of RBD-LCB1 and Mpro-2JOS complexes with an average RMSD of 1.902 and 2.476 respectively. We ascertain that LCB1 and 2JOS peptides are promising inhibitors to combat emerging variants of SARS-CoV-2 and thus warrant further investigations using in-vitro and in-vivo analysis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Roshny Prasad
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Harikrishnan Ajith
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | | | | | - Anand Mohan
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Shijulal Nelson-Sathi
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
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10
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Ghoula M, Deyawe Kongmeneck A, Eid R, Camproux AC, Moroy G. Comparative Study of the Mutations Observed in the SARS-CoV-2 RBD Variants of Concern and Their Impact on the Interaction with the ACE2 Protein. J Phys Chem B 2023; 127:8586-8602. [PMID: 37775095 PMCID: PMC10578311 DOI: 10.1021/acs.jpcb.3c01467] [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: 03/02/2023] [Revised: 04/20/2023] [Indexed: 10/01/2023]
Abstract
SARS-CoV-2 strains have made an appearance across the globe, causing over 757 million cases and over 6.85 million deaths at the time of writing. The emergence of these variants shows the amplitude of genetic variation to which the wild-type strains have been subjected. The rise of the different SARS-CoV-2 variants resulting from such genetic modification has significantly affected COVD-19's major impact on proliferation, virulence, and clinics. With the emergence of the variants of concern, the spike protein has been identified as a possible therapeutic target due to its critical role in binding to human cells and pathogenesis. These mutations could be linked to functional heterogeneity and use a different infection strategy. For example, the Omicron variant's multiple mutations should be carefully examined, as they represent one of the most widely spread strains and hint to us that there may be more genetic changes in the virus. As a result, we applied a common protocol where we reconstructed SARS-CoV-2 variants of concern and performed molecular dynamics simulations to study the stability of the ACE2-RBD complex in each variant. We also carried out free energy calculations to compare the binding and biophysical properties of the different SARS-CoV-2 variants when they interact with ACE2. Therefore, we were able to obtain consistent results and uncover new crucial residues that were essential for preserving a balance between maintaining a high affinity for ACE2 and the capacity to evade RBD-targeted antibodies. Our detailed structural analysis showed that SARS-CoV-2 variants of concern show a higher affinity for ACE2 compared to the Wuhan strain. Additionally, residues K417N and E484K/A might play a crucial role in antibody evasion, whereas Q498R and N501Y are specifically mutated to strengthen RBD affinity to ACE2 and, thereby, increase the viral effect of the COVID-19 virus.
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Affiliation(s)
- Mariem Ghoula
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Audrey Deyawe Kongmeneck
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Rita Eid
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Anne-Claude Camproux
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Gautier Moroy
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
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11
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Miteva D, Kitanova M, Batselova H, Lazova S, Chervenkov L, Peshevska-Sekulovska M, Sekulovski M, Gulinac M, Vasilev GV, Tomov L, Velikova T. The End or a New Era of Development of SARS-CoV-2 Virus: Genetic Variants Responsible for Severe COVID-19 and Clinical Efficacy of the Most Commonly Used Vaccines in Clinical Practice. Vaccines (Basel) 2023; 11:1181. [PMID: 37514997 PMCID: PMC10385722 DOI: 10.3390/vaccines11071181] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/22/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Although the chief of the World Health Organization (WHO) has declared the end of the coronavirus disease 2019 (COVID-19) as a global health emergency, the disease is still a global threat. To be able to manage such pandemics in the future, it is necessary to develop proper strategies and opportunities to protect human life. The data on the SARS-CoV-2 virus must be continuously analyzed, and the possibilities of mutation and the emergence of new, more infectious variants must be anticipated, as well as the options of using different preventive and therapeutic techniques. This is because the fast development of severe acute coronavirus 2 syndrome (SARS-CoV-2) variants of concern have posed a significant problem for COVID-19 pandemic control using the presently available vaccinations. This review summarizes data on the SARS-CoV-2 variants that are responsible for severe COVID-19 and the clinical efficacy of the most commonly used vaccines in clinical practice. The consequences after the disease (long COVID or post-COVID conditions) continue to be the subject of studies and research, and affect social and economic life worldwide.
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Affiliation(s)
- Dimitrina Miteva
- Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", 8 Dragan Tzankov str., 1164 Sofia, Bulgaria
| | - Meglena Kitanova
- Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", 8 Dragan Tzankov str., 1164 Sofia, Bulgaria
| | - Hristiana Batselova
- Department of Epidemiology and Disaster Medicine, University Hospital "Saint George", Medical University, 6000 Plovdiv, Bulgaria
| | - Snezhina Lazova
- Pediatric Department, University Hospital "N. I. Pirogov," 21 "General Eduard I. Totleben" Blvd, 1606 Sofia, Bulgaria
- Department of Healthcare, Faculty of Public Health "Prof. Tsekomir Vodenicharov, MD, DSc", Medical University of Sofia, Bialo More 8 str., 1527 Sofia, Bulgaria
| | - Lyubomir Chervenkov
- Department of Diagnostic Imaging, Medical University Plovdiv, Bul. Vasil Aprilov 15A, 4000 Plovdiv, Bulgaria
| | - Monika Peshevska-Sekulovska
- Department of Gastroenterology, University Hospital Lozenetz, 1407 Sofia, Bulgaria
- Medical Faculty, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria
| | - Metodija Sekulovski
- Medical Faculty, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria
- Department of Anesthesiology and Intensive Care, University Hospital Lozenetz, 1 Kozyak str., 1407 Sofia, Bulgaria
| | - Milena Gulinac
- Department of General and Clinical Pathology, Medical University of Plovdiv, Bul. Vasil Aprilov 15A, 4000 Plovdiv, Bulgaria
| | - Georgi V Vasilev
- Clinic of Endocrinology and Metabolic Disorders, UMHAT "Sv. Georgi", 4000 Plovdiv, Bulgaria
| | - Luchesar Tomov
- Department of Informatics, New Bulgarian University, Montevideo 21 str., 1618 Sofia, Bulgaria
| | - Tsvetelina Velikova
- Medical Faculty, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria
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12
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Shajahan A, Pepi LE, Kumar B, Murray NB, Azadi P. Site specific N- and O-glycosylation mapping of the spike proteins of SARS-CoV-2 variants of concern. Sci Rep 2023; 13:10053. [PMID: 37344512 PMCID: PMC10284906 DOI: 10.1038/s41598-023-33088-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 04/06/2023] [Indexed: 06/23/2023] Open
Abstract
The glycosylation on the spike (S) protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, modulates the viral infection by altering conformational dynamics, receptor interaction and host immune responses. Several variants of concern (VOCs) of SARS-CoV-2 have evolved during the pandemic, and crucial mutations on the S protein of the virus have led to increased transmissibility and immune escape. In this study, we compare the site-specific glycosylation and overall glycomic profiles of the wild type Wuhan-Hu-1 strain (WT) S protein and five VOCs of SARS-CoV-2: Alpha, Beta, Gamma, Delta and Omicron. Interestingly, both N- and O-glycosylation sites on the S protein are highly conserved among the spike mutant variants, particularly at the sites on the receptor-binding domain (RBD). The conservation of glycosylation sites is noteworthy, as over 2 million SARS-CoV-2 S protein sequences have been reported with various amino acid mutations. Our detailed profiling of the glycosylation at each of the individual sites of the S protein across the variants revealed intriguing possible association of glycosylation pattern on the variants and their previously reported infectivity. While the sites are conserved, we observed changes in the N- and O-glycosylation profile across the variants. The newly emerged variants, which showed higher resistance to neutralizing antibodies and vaccines, displayed a decrease in the overall abundance of complex-type glycans with both fucosylation and sialylation and an increase in the oligomannose-type glycans across the sites. Among the variants, the glycosylation sites with significant changes in glycan profile were observed at both the N-terminal domain and RBD of S protein, with Omicron showing the highest deviation. The increase in oligomannose-type happens sequentially from Alpha through Delta. Interestingly, Omicron does not contain more oligomannose-type glycans compared to Delta but does contain more compared to the WT and other VOCs. O-glycosylation at the RBD showed lower occupancy in the VOCs in comparison to the WT. Our study on the sites and pattern of glycosylation on the SARS-CoV-2 S proteins across the VOCs may help to understand how the virus evolved to trick the host immune system. Our study also highlights how the SARS-CoV-2 virus has conserved both N- and O- glycosylation sites on the S protein of the most successful variants even after undergoing extensive mutations, suggesting a correlation between infectivity/ transmissibility and glycosylation.
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Affiliation(s)
- Asif Shajahan
- Vaccine Production Program, Vaccine Research Center, National Institutes of Health, 9 W Watkins Mill Rd, Gaithersburg, MD, 20877, USA.
| | - Lauren E Pepi
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - Bhoj Kumar
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - Nathan B Murray
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA.
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13
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Saldivar-Espinoza B, Garcia-Segura P, Novau-Ferré N, Macip G, Martínez R, Puigbò P, Cereto-Massagué A, Pujadas G, Garcia-Vallve S. The Mutational Landscape of SARS-CoV-2. Int J Mol Sci 2023; 24:ijms24109072. [PMID: 37240420 DOI: 10.3390/ijms24109072] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Mutation research is crucial for detecting and treating SARS-CoV-2 and developing vaccines. Using over 5,300,000 sequences from SARS-CoV-2 genomes and custom Python programs, we analyzed the mutational landscape of SARS-CoV-2. Although almost every nucleotide in the SARS-CoV-2 genome has mutated at some time, the substantial differences in the frequency and regularity of mutations warrant further examination. C>U mutations are the most common. They are found in the largest number of variants, pangolin lineages, and countries, which indicates that they are a driving force behind the evolution of SARS-CoV-2. Not all SARS-CoV-2 genes have mutated in the same way. Fewer non-synonymous single nucleotide variations are found in genes that encode proteins with a critical role in virus replication than in genes with ancillary roles. Some genes, such as spike (S) and nucleocapsid (N), show more non-synonymous mutations than others. Although the prevalence of mutations in the target regions of COVID-19 diagnostic RT-qPCR tests is generally low, in some cases, such as for some primers that bind to the N gene, it is significant. Therefore, ongoing monitoring of SARS-CoV-2 mutations is crucial. The SARS-CoV-2 Mutation Portal provides access to a database of SARS-CoV-2 mutations.
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Affiliation(s)
- Bryan Saldivar-Espinoza
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Pol Garcia-Segura
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Nil Novau-Ferré
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Guillem Macip
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | | | - Pere Puigbò
- Department of Biology, University of Turku, 20500 Turku, Finland
- Department of Biochemistry and Biotechnology, Rovira i Virgili University, 43007 Tarragona, Spain
- Eurecat, Technology Centre of Catalonia, Unit of Nutrition and Health, 43204 Reus, Spain
| | - Adrià Cereto-Massagué
- EURECAT Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain
| | - Gerard Pujadas
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Santiago Garcia-Vallve
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
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14
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Luo Y, Liu S, Xue J, Yang Y, Zhao J, Sun Y, Wang B, Yin S, Li J, Xia Y, Ge F, Dong J, Guo L, Ye B, Huang W, Wang Y, Xi JJ. High-throughput screening of spike variants uncovers the key residues that alter the affinity and antigenicity of SARS-CoV-2. Cell Discov 2023; 9:40. [PMID: 37041132 PMCID: PMC10088716 DOI: 10.1038/s41421-023-00534-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/03/2023] [Indexed: 04/13/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has elicited a worldwide pandemic since late 2019. There has been ~675 million confirmed coronavirus disease 2019 (COVID-19) cases, leading to more than 6.8 million deaths as of March 1, 2023. Five SARS-CoV-2 variants of concern (VOCs) were tracked as they emerged and were subsequently characterized. However, it is still difficult to predict the next dominant variant due to the rapid evolution of its spike (S) glycoprotein, which affects the binding activity between cellular receptor angiotensin-converting enzyme 2 (ACE2) and blocks the presenting epitope from humoral monoclonal antibody (mAb) recognition. Here, we established a robust mammalian cell-surface-display platform to study the interactions of S-ACE2 and S-mAb on a large scale. A lentivirus library of S variants was generated via in silico chip synthesis followed by site-directed saturation mutagenesis, after which the enriched candidates were acquired through single-cell fluorescence sorting and analyzed by third-generation DNA sequencing technologies. The mutational landscape provides a blueprint for understanding the key residues of the S protein binding affinity to ACE2 and mAb evasion. It was found that S205F, Y453F, Q493A, Q493M, Q498H, Q498Y, N501F, and N501T showed a 3-12-fold increase in infectivity, of which Y453F, Q493A, and Q498Y exhibited at least a 10-fold resistance to mAbs REGN10933, LY-CoV555, and REGN10987, respectively. These methods for mammalian cells may assist in the precise control of SARS-CoV-2 in the future.
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Affiliation(s)
- Yufeng Luo
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Shuo Liu
- Graduate School of Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | - Jiguo Xue
- Institute of Health Service and Transfusion Medicine, Beijing, China
| | - Ye Yang
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Junxuan Zhao
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Ying Sun
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Bolun Wang
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Shenyi Yin
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Juan Li
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Yuchao Xia
- GeneX Health Co. Ltd, Beijing, China
- College of Science, Beijing Information Science and Technology University, Beijing, China
| | - Feixiang Ge
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | | | - Lvze Guo
- GeneX Health Co. Ltd, Beijing, China
| | - Buqing Ye
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, 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, China
| | - Youchun Wang
- Graduate School of Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China.
| | - Jianzhong Jeff Xi
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China.
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15
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Wang W, Hu Y, Li B, Wang H, Shen J. Applications of nanobodies in the prevention, detection, and treatment of the evolving SARS-CoV-2. Biochem Pharmacol 2023; 208:115401. [PMID: 36592707 PMCID: PMC9801699 DOI: 10.1016/j.bcp.2022.115401] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022]
Abstract
Global health and economy are deeply influenced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its newly emerging variants. Nanobodies with nanometer-scale size are promising for the detection and treatment of SARS-CoV-2 and its variants because they are superior to conventional antibodies in terms of cryptic epitope accessibility, tissue penetration, cost, formatting adaptability, and especially protein stability, which enables their aerosolized specific delivery to lung tissues. This review summarizes the progress in the prevention, detection, and treatment of SARS-CoV-2 using nanobodies, as well as strategies to combat the evolving SARS-CoV-2 variants. Generally, highly efficient generation of potent broad-spectrum nanobodies targeting conserved epitopes or further construction of multivalent formats targeting non-overlapping epitopes can promote neutralizing activity against SARS-CoV-2 variants and suppress immune escape.
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Affiliation(s)
- Wenyi Wang
- Institute for Medical Biology and Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, Hubei 430074, PR China,Corresponding author
| | - Yue Hu
- Institute for Medical Biology and Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, Hubei 430074, PR China
| | - Bohan Li
- Institute for Medical Biology and Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, Hubei 430074, PR China
| | - Huanan Wang
- Department of Respiratory Medicine, The 990th Hospital of Joint Logistics Support Force, Zhumadian, Henan 463000, PR China
| | - Jinhua Shen
- Institute for Medical Biology and Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, Hubei 430074, PR China
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16
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Xu H, Wang T, Sun P, Hou X, Gong X, Zhang B, Wu J, Liu B. A bivalent subunit vaccine efficiently produced in Pichia pastoris against SARS-CoV-2 and emerging variants. Front Microbiol 2023; 13:1093080. [PMID: 36704561 PMCID: PMC9871450 DOI: 10.3389/fmicb.2022.1093080] [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: 11/08/2022] [Accepted: 12/16/2022] [Indexed: 01/11/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus type II (SARS-CoV-2) variants have led to a decline in the protection of existing vaccines and antibodies, and there is an urgent need for a broad-spectrum vaccination strategy to reduce the pressure on the prevention and control of the pandemic. In this study, the receptor binding domain (RBD) of the SARS-CoV-2 Beta variant was successfully expressed through a glycoengineered yeast platform. To pursue a more broad-spectrum vaccination strategy, RBD-Beta and RBD-wild type were mixed at the ratio of 1:1 with Al(OH)3 and CpG double adjuvants for the immunization of BALB/c mice. This bivalent vaccine stimulated robust conjugated antibody titers and a broader spectrum of neutralizing antibody titers. These results suggested that a bivalent vaccine of RBD-Beta and RBD-wild type could be a possible broad-spectrum vaccination strategy.
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Affiliation(s)
| | | | | | | | | | | | - Jun Wu
- *Correspondence: Jun Wu, ✉
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17
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Wu W, Cheng Y, Zhou H, Sun C, Zhang S. The SARS-CoV-2 nucleocapsid protein: its role in the viral life cycle, structure and functions, and use as a potential target in the development of vaccines and diagnostics. Virol J 2023; 20:6. [PMID: 36627683 PMCID: PMC9831023 DOI: 10.1186/s12985-023-01968-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) continues to take a heavy toll on personal health, healthcare systems, and economies around the globe. Scientists are expending tremendous effort to develop diagnostic technologies for detecting positive infections within the shortest possible time, and vaccines and drugs specifically for the prevention and treatment of COVID-19 disease. At the same time, emerging novel variants have raised serious concerns about vaccine efficacy. The SARS-CoV-2 nucleocapsid (N) protein plays an important role in the coronavirus life cycle, and participates in various vital activities after virus invasion. It has attracted a large amount of attention for vaccine and drug development. Here, we summarize the latest research of the N protein, including its role in the SARS-CoV-2 life cycle, structure and function, and post-translational modifications in addition to its involvement in liquid-liquid phase separation (LLPS) and use as a basis for the development of vaccines and diagnostic techniques.
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Affiliation(s)
- Wenbing Wu
- grid.410578.f0000 0001 1114 4286Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000 China
| | - Ying Cheng
- grid.410578.f0000 0001 1114 4286Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000 China
| | - Hong Zhou
- grid.410578.f0000 0001 1114 4286Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000 China
| | - Changzhen Sun
- grid.410578.f0000 0001 1114 4286Drug Research Center of Integrated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000 China
| | - Shujun Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China.
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18
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Mousavi SF, Ebrahimi M, Moghaddam SAA, Moafi N, Jafari M, Tavakolian A, Heidary M. Evaluating the characteristics of patients with SARS-CoV-2 infection admitted during COVID-19 peaks: A single-center study. VACUNAS 2023; 24:27-36. [PMID: 36062028 PMCID: PMC9424515 DOI: 10.1016/j.vacun.2022.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/13/2022] [Indexed: 02/08/2023]
Abstract
Background Nowadays, the world is facing a coronavirus disease (COVID-19) pandemic, elicited by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). At the time of studying, five COVID-19 waves occurred in Iran. We aimed to evaluate the characteristics of patients with SARS-CoV-2 infection admitted to Vasei Hospital of Sabzevar, Iran during COVID-19 peaks. Methods Clinical manifestations, laboratory findings, radiological findings, and underlying diseases of patients with COVID-19 were obtained from electronic medical records. Then, this information was compared in patients with SARS-CoV-2 infection to the peaks of COVID-19. Results The highest and lowest respiratory involvements were observed in the third (74.6%) and fourth (38.8%) peaks, respectively. The most common radiological finding in all peaks was ground-glass opacity (28.98%), followed by consolidation, which was the highest (14.6%) in peak three. The lymphocyte count decreased in all peaks. Its highest reduction (16.12) occurred in the third peak. The SpO2 was lower than normal range in all peaks, except for the second (90.77%) and fifth (91.06%) peaks. Dyspnea (52.36%) was the most and dizziness (1.26%) and sore throat (0.6%) were the least frequent symptoms. The mortality rates were 14. 4%, 18.2%, 23%, 9.02%, and 9.4% in the first to fifth peaks, respectively. Conclusion As different variants of the SARS-CoV-2 virus were predominant in each wave, COVID-19 patients had different features in various peaks. The fifth wave of COVID-19 had the highest number of hospitalized patients, while the first peak had the lowest number. Perhaps, the significant increase in testing capacity in the fifth wave and its long time period are the reasons for this growth. Most of the clinical symptoms were similar in all peaks, but the incidence was different. As patients hospitalized in the third peak had the highest rate of underlying disease, it can be a reason for the increase in the death rate of patients. We did not observe any significant differences in laboratory tests among the patients during different peaks. Thus, we should be vigilant in continuously studying the characteristics of the disease, and be able to modify treatments rapidly if necessary.
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Affiliation(s)
| | | | | | - Narges Moafi
- Student Research Committee, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Mahbobe Jafari
- Student Research Committee, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Ayoub Tavakolian
- Emergency Medicine Department, Faculty of Medicine, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Mohsen Heidary
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran,Corresponding authors
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19
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Mousavi SF, Ebrahimi M, Moghaddam SAA, Moafi N, Jafari M, Tavakolian A, Heidary M. Evaluating the characteristics of patients with SARS-CoV-2 infection admitted during COVID-19 peaks: A single-center study. VACUNAS (ENGLISH EDITION) 2023; 24. [PMCID: PMC9969536 DOI: 10.1016/j.vacune.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Background Nowadays, the world is facing a coronavirus disease (COVID-19) pandemic, elicited by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). At the time of studying, five COVID-19 waves occurred in Iran. We aimed to evaluate the characteristics of patients with SARS-CoV-2 infection admitted to Vasei Hospital of Sabzevar, Iran during COVID-19 peaks. Methods Clinical manifestations, laboratory findings, radiological findings, and underlying diseases of patients with COVID-19 were obtained from electronic medical records. Then, this information was compared in patients with SARS-CoV-2 infection to the peaks of COVID-19. Results The highest and lowest respiratory involvements were observed in the third (74.6%) and fourth (38.8%) peaks, respectively. The most common radiological finding in all peaks was ground-glass opacity (28.98%), followed by consolidation, which was the highest (14.6%) in peak three. The lymphocyte count decreased in all peaks. Its highest reduction (16.12) occurred in the third peak. The SpO2 was lower than normal range in all peaks, except for the second (90.77%) and fifth (91.06%) peaks. Dyspnea (52.36%) was the most and dizziness (1.26%) and sore throat (0.6%) were the least frequent symptoms. The mortality rates were 14. 4%, 18.2%, 23%, 9.02%, and 9.4% in the first to fifth peaks, respectively. Conclusion As different variants of the SARS-CoV-2 virus were predominant in each wave, COVID-19 patients had different features in various peaks. The fifth wave of COVID-19 had the highest number of hospitalized patients, while the first peak had the lowest number. Perhaps, the significant increase in testing capacity in the fifth wave and its long time period are the reasons for this growth. Most of the clinical symptoms were similar in all peaks, but the incidence was different. As patients hospitalized in the third peak had the highest rate of underlying disease, it can be a reason for the increase in the death rate of patients. We did not observe any significant differences in laboratory tests among the patients during different peaks. Thus, we should be vigilant in continuously studying the characteristics of the disease, and be able to modify treatments rapidly if necessary.
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Affiliation(s)
| | | | | | - Narges Moafi
- Student Research Committee, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Mahbobe Jafari
- Student Research Committee, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Ayoub Tavakolian
- Emergency Medicine Department, Faculty of Medicine, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Mohsen Heidary
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran,Corresponding authors
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20
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Green and efficient one-pot three-component synthesis of novel drug-like furo[2,3–d]pyrimidines as potential active site inhibitors and putative allosteric hotspots modulators of both SARS-CoV-2 MPro and PLPro. Bioorg Chem 2023; 135:106390. [PMID: 37037129 PMCID: PMC9883075 DOI: 10.1016/j.bioorg.2023.106390] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/29/2023]
Abstract
In this paper, an environmentally benign, convenient, and efficient one-pot three-component reaction has been developed for the regioselective synthesis of novel 5-aroyl(or heteroaroyl)-6-(alkylamino)-1,3-dimethylfuro[2,3-d]pyrimidine-2,4(1H,3H)-diones (4a‒n) through the sequential condensation of aryl(or heteroaryl)glyoxal monohydrates (1a‒g), 1,3-dimethylbarbituric acid (2), and alkyl(viz. cyclohexyl or tert-butyl)isocyanides (3a or 3b) catalyzed by ultra-low loading ZrOCl2•8H2O (just 2 mol%) in water at 50 ˚C. After synthesis and characterization of the mentioned furo[2,3-d]pyrimidines (4a‒n), their multi-targeting inhibitory properties were investigated against the active site and putative allosteric hotspots of both SARS-CoV-2 main protease (MPro) and papain-like protease (PLPro) based on molecular docking studies and compare the attained results with various medicinal compounds which approximately in three past years were used, introduced, and or repurposed to fight against COVID-19. Furthermore, drug-likeness properties of the mentioned small heterocyclic frameworks (4a‒n) have been explored using in silico ADMET analyses. Interestingly, the molecular docking studies and ADMET-related data revealed that the novel series of furo[2,3-d]pyrimidines (4a‒n), especially 5-(3,4-methylendioxybenzoyl)-6-(cyclohexylamino)-1,3-dimethylfuro[2,3-d]pyrimidine-2,4(1H,3H)-dione (4g) as hit one is potential COVID-19 drug candidate, can subject to further in vitro and in vivo studies. It is worthwhile to note that the protein-ligand-type molecular docking studies on the human body temperature-dependent MPro protein that surprisingly contains zincII (ZnII) ion between His41/Cys145 catalytic dyad in the active site, which undoubtedly can make new plans for designing novel SARS-CoV-2 MPro inhibitors, is performed for the first time in this paper, to the best of our knowledge.
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21
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He DC, He CQ. Discovery of vaccine-like recombinant SARS-CoV-2 circulating in human. Virol J 2022; 19:209. [PMID: 36482293 PMCID: PMC9733243 DOI: 10.1186/s12985-022-01945-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022] Open
Abstract
For viral diseases, vaccination with live attenuated vaccine (LAV) is one of the most effective means for fighting the diseases. However, LAV occasionally overflows from vaccinated individuals circulate in the population with unforeseen consequences. Currently, SARS-CoV-2 LAVs are undergoing clinical trials. In this study, we found that the viruses isolated from Indian SARS CoV-2 infected persons may be candidate LAV-derived strains, indicating the risk of SARS-CoV-2 LAV spillover from vaccinated persons, increasing the complexity of SARS-CoV-2 detection. In addition, the property of frequent recombination of SARS-CoV-2 increases the chance of LAV virulence reversion. Therefore, how to distinguish the LAV viruses from the wild strain and how to avoid the recombination of the circulating vaccine strain and the wild strain are the challenges currently faced by SARS CoV-2 LAV development.
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Affiliation(s)
- Daniel Chang He
- grid.410585.d0000 0001 0495 1805International Department, High School Attached to Shandong Normal University, Jinan, 250014 China
| | - Cheng-Qiang He
- grid.410585.d0000 0001 0495 1805Dongying Institute, Shandong Normal University, Dongying, 257000 China ,grid.410585.d0000 0001 0495 1805Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Science, Shandong Normal University, Jinan, 250014 Shandong Province China
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22
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Dhawan M, Sharma A, Priyanka, Thakur N, Rajkhowa TK, Choudhary OP. Delta variant (B.1.617.2) of SARS-CoV-2: Mutations, impact, challenges and possible solutions. Hum Vaccin Immunother 2022; 18:2068883. [PMID: 35507895 PMCID: PMC9359381 DOI: 10.1080/21645515.2022.2068883] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/04/2022] [Accepted: 04/18/2022] [Indexed: 12/24/2022] Open
Abstract
Since commencement of COVID-19 pandemic, several SARS-CoV-2 variants have emerged amid containment efforts via vaccination. The Delta variant (B.1.617.2), discovered in October 2020, was designated as a VOC by the WHO on May 11, 2021. The enhanced transmissibility of Delta variant has been associated with critical mutations such as D614G, L452R, P681R, and T478K in the S-protein. The increased affinity of the S-protein and ACE2 has been postulated as a key reason for decreased vaccine efficacy. As per evidence, the Delta variant possesses increased transmissibility and decreased vaccine efficacy compared to other VOCs like Alpha and Beta. This has led to concerns regarding the acquisition of novel mutations in the Delta variant and outbreaks in vulnerable communities, including vaccinated people. In this mini-review of Delta variant, we have explained its evolution and characteristics, the impact of spike mutations on infectivity and immune evasion, and measures to combat future outbreaks.
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Affiliation(s)
- Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana, India
- Trafford College, Altrincham, Manchester, UK
| | - Abhilasha Sharma
- Department of Life Science, University School of Sciences, Gujarat University, Ahmedabad, India
| | - Priyanka
- Independent Researcher, 07, Type IV Quarter, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, Mizoram, India
| | - Nanamika Thakur
- Department of Medical Lab Technology, Faculty of Allied and Healthcare Sciences, GNA University, Phagwara, Punjab, India
| | - Tridib Kumar Rajkhowa
- Department of Veterinary Pathology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, Mizoram, India
| | - Om Prakash Choudhary
- Department of Veterinary Anatomy and Histology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, Mizoram, India
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23
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Shajahan A, Pepi L, Kumar B, Murray N, Azadi P. Site Specific N- and O-glycosylation mapping of the Spike Proteins of SARS-CoV-2 Variants of Concern.. [PMID: 36415454 PMCID: PMC9681045 DOI: 10.21203/rs.3.rs-2188138/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The glycosylation on the spike (S) protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, modulates the viral infection by altering conformational dynamics, receptor interaction and host immune responses. Several variants of concern (VOCs) of SARS-CoV-2 have evolved during the pandemic, and crucial mutations on the S protein of the virus led to increased transmissibility and immune escape. In this study, we compare the site-specific glycosylation and overall glycomic profile of the wild type Wuhan-Hu-1 strain (WT) S protein and five VOCs of SARS-CoV-2: Alpha, Beta, Gamma, Delta and Omicron. Interestingly, both N- and O-glycosylation sites on the S protein are highly conserved among the spike mutant variants, particularly at the sites on the receptor-binding domain (RBD). The conservation of glycosylation sites is noteworthy, as over 2 million SARS-CoV-2 S protein sequences have been reported with various amino acid mutations. Our detailed profiling of the glycosylation at each of the individual sites of the S protein across the variants revealed intriguing possible association of glycosylation pattern on the variants and their previously reported infectivity. While the sites are conserved, we observed changes in the N- and O-glycosylation profile across the variants. The newly emerged variants, which showed higher resistance to neutralizing antibodies and vaccines, displayed a decrease in the overall abundance of complex-type glycans with both fucosylation and sialylation and an increase in the oligomannose-type glycans across the sites. Among the variants, the glycosylation sites with significant changes in glycan profile were observed at both the N-terminal domain (NTD) and RBD of S protein, with Omicron showing the highest deviation. The increase in oligomannose-type happens sequentially from Alpha through Delta. Interestingly, Omicron does not contain more oligomannose-type glycans compared to Delta but does contain more compared to the WT and other VOCs. O-glycosylation at the RBD showed lower occupancy in the VOCs in comparison to the WT. Our study on the sites and pattern of glycosylation on the SARS-CoV-2 S proteins across the VOCs may help to understand how the virus evolved to trick the host immune system. Our study also highlights how the SARS-CoV-2 virus has conserved both N- and O- glycosylation sites on the S protein of the most successful variants even after undergoing extensive mutations, suggesting a correlation between infectivity/transmissibility and glycosylation.
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24
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O’Donnell KL, Gourdine T, Fletcher P, Clancy CS, Marzi A. Protection from COVID-19 with a VSV-based vaccine expressing the spike and nucleocapsid proteins. Front Immunol 2022; 13:1025500. [PMID: 36353642 PMCID: PMC9638159 DOI: 10.3389/fimmu.2022.1025500] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/04/2022] [Indexed: 11/24/2022] Open
Abstract
Successful vaccine efforts countering the COVID-19 pandemic are centralized around the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein as viral antigen and have greatly reduced the morbidity and mortality associated with COVID-19. Since the start of this pandemic, SARS-CoV-2 has evolved resulting in new variants of concern (VOC) challenging the vaccine-established immunologic memory. We show that vaccination with a vesicular stomatitis virus (VSV)-based vaccine expressing the SARS-CoV-2 S plus the conserved nucleocapsid (N) protein was protective in a hamster challenge model when a single dose was administered 28 or 10 days prior to challenge, respectively. In this study, only intranasal vaccination resulted in protection against challenge with multiple VOC highlighting that the addition of the N protein indeed improved protective efficacy. This data demonstrates the ability of a VSV-based dual-antigen vaccine to reduce viral shedding and protect from disease caused by SARS-CoV-2 VOC.
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Affiliation(s)
- Kyle L. O’Donnell
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Tylisha Gourdine
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Paige Fletcher
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Chad S. Clancy
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
- *Correspondence: Andrea Marzi,
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A Vaccine with Multiple Receptor-Binding Domain Subunit Mutations Induces Broad-Spectrum Immune Response against SARS-CoV-2 Variants of Concern. Vaccines (Basel) 2022; 10:vaccines10101653. [PMID: 36298518 PMCID: PMC9609383 DOI: 10.3390/vaccines10101653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/24/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022] Open
Abstract
With the emergence of more variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the immune evasion of these variants from existing vaccines, the development of broad-spectrum vaccines is urgently needed. In this study, we designed a novel SARS-CoV-2 receptor-binding domain (RBD) subunit (RBD5m) by integrating five important mutations from SARS-CoV-2 variants of concern (VOCs). The neutralization activities of antibodies induced by the RBD5m candidate vaccine are more balanced and effective for neutralizing different SARS-CoV-2 VOCs in comparison with those induced by the SARS-CoV-2 prototype strain RBD. Our results suggest that the RBD5m vaccine is a good broad-spectrum vaccine candidate able to prevent disease from several different SARS-CoV-2 VOCs.
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Molecular Characterization of Whole-Genome SARS-CoV-2 from the First Suspected Cases of the XE Variant in the Lazio Region, Italy. Diagnostics (Basel) 2022; 12:diagnostics12092219. [PMID: 36140622 PMCID: PMC9497488 DOI: 10.3390/diagnostics12092219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/02/2022] [Accepted: 09/10/2022] [Indexed: 11/30/2022] Open
Abstract
We report two cases of SARS-CoV-2 recombinant variant XE detected in nasopharyngeal swabs (NPS) of hospitalized patients with no evident epidemiological link in Lazio, Central Italy. Whole-Genome Sequencing (WGS) performed on an Ion Torrent GSS5 platform according to Italian flash surveys showed genomes corresponding to the PANGOLIN unclassified lineage and the Nextclade XE clade. Further analyses were then carried out to investigate more deeply the genetic characteristics of these XE-like sequences. When phylogenetic trees, by using IQ-TREE, were built splitting the genome into two regions according to the putative XE recombination site, the upstream and downstream regions were seen to be clustered near BA.1 and BA.2 sequences, respectively. However, our XE-like sequences clustered separately, with a significant bootstrap, from the classified European and Italian XE strains, although the recombination site between BA.1 and BA.2 was identified at the nucleotide site 11556 by RDP4 software, consistent with the putative XE breakpoint. These findings show the risk of the introduction of novel recombinant variants of SARS-CoV-2 and the existence of XE-like strains, phylogenetically separated, that could make their exact taxonomy difficult. It follows the need for continued SARS-CoV-2 surveillance by WGS.
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SARS-CoV-2 Spike Does Not Possess Intrinsic Superantigen-like Inflammatory Activity. Cells 2022; 11:cells11162526. [PMID: 36010602 PMCID: PMC9406418 DOI: 10.3390/cells11162526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 08/12/2022] [Indexed: 11/24/2022] Open
Abstract
Multisystem inflammatory syndrome in children (MIS-C) is a rare hyperinflammatory disease occurring several weeks after SARS-CoV-2 infection. The clinical similarities between MIS-C and the toxic shock syndrome, together with the preferential expansion of T cells with a T-cell receptor variable β chain (TCRVβ) skewing, suggested a superantigen theory of MIS-C. For instance, recent in silico modelling evidenced the presence of a highly conserved motif within SARS-CoV-2 spike protein similar in structure to the superantigenic fragment of staphylococcal enterotoxin B (SEB). However, experimental data on the superantigenic activity of the SARS-CoV-2 spike have not yet been provided. Here, we assessed the superantigenic activity of the SARS-CoV-2 spike by analysing inflammatory cytokine production in both Jurkat cells and the peripheral blood CD4+ T cells stimulated with the SARS-CoV-2 spike or SEB as a control. We found that, unlike SEB, the SARS-CoV-2 spike does not exhibit an intrinsic superantigen-like activity.
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Chakraborty C, Bhattacharya M, Sharma AR, Mallik B. Omicron (B.1.1.529) - A new heavily mutated variant: Mapped location and probable properties of its mutations with an emphasis on S-glycoprotein. Int J Biol Macromol 2022; 219:980-997. [PMID: 35952818 PMCID: PMC9359758 DOI: 10.1016/j.ijbiomac.2022.07.254] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/23/2022] [Accepted: 07/31/2022] [Indexed: 12/17/2022]
Abstract
Omicron, another SARS-CoV-2 variant, has been recorded and reported as a VoC. It has already spread across >30 countries and is a highly mutated variant. We tried to understand the role of mutations in the investigated variants by comparison with previous characterized VoC. We have mapped the mutations in Omicron S-glycoprotein's secondary and tertiary structure landscape using bioinformatics tools and statistical software and developed different models. In addition, we analyzed the effect of diverse mutations in antibody binding regions of the S-glycoprotein on the binding affinity of the investigated antibodies. This study has chosen eight significant mutations in Omicron (D614G, E484A, N501Y, Q493K, K417N, S477N, Y505H G496S), and seven of them are located in the RBD region. We also performed a comparative analysis of the ΔΔG score of these mutations to understand the stabilizing or destabilizing properties of the investigated mutations. The analysis outcome shows that D614G, Q493K, and S477N mutations are stable mutations with ΔΔG scores of 0.351 kcal/mol, 0.470 kcal/mol, and 0.628 kcal/mol, respectively, according to DynaMut estimations. While other mutations (E484A, N501Y, K417N, Y505H, G496S) showed destabilizing results. The D614G, E484A, N501Y, K417N, Y505H, and G496S mutations increased the molecular flexibility of S-glycoprotein to interact with the ACE2 receptor, increasing the variant's infectivity. Our study will contribute to research on the SARS-CoV-2 variant, Omicron, by providing information on the mutational pattern and exciting properties of these eight significant mutations, such as antibody escape and infectivity quotient (stabilizing or destabilizing; increased or decreased molecular flexibility of S-glycoprotein to interact with the human ACE2 receptor).
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India.
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, South Korea
| | - Bidyut Mallik
- Department of Applied Science, Galgotias College of Engineering and Technology, Knowledge Park-II, Greater Noida, Uttar Pradesh 201306, India
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Rubio-Casillas A, Redwan EM, Uversky VN. SARS-CoV-2: A Master of Immune Evasion. Biomedicines 2022; 10:biomedicines10061339. [PMID: 35740361 PMCID: PMC9220273 DOI: 10.3390/biomedicines10061339] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/03/2022] [Accepted: 06/04/2022] [Indexed: 02/07/2023] Open
Abstract
Viruses and their hosts have coevolved for a long time. This coevolution places both the pathogen and the human immune system under selective pressure; on the one hand, the immune system has evolved to combat viruses and virally infected cells, while viruses have developed sophisticated mechanisms to escape recognition and destruction by the immune system. SARS-CoV-2, the pathogen that is causing the current COVID-19 pandemic, has shown a remarkable ability to escape antibody neutralization, putting vaccine efficacy at risk. One of the virus’s immune evasion strategies is mitochondrial sabotage: by causing reactive oxygen species (ROS) production, mitochondrial physiology is impaired, and the interferon antiviral response is suppressed. Seminal studies have identified an intra-cytoplasmatic pathway for viral infection, which occurs through the construction of tunneling nanotubes (TNTs), hence enhancing infection and avoiding immune surveillance. Another method of evading immune monitoring is the disruption of the antigen presentation. In this scenario, SARS-CoV-2 infection reduces MHC-I molecule expression: SARS-CoV-2’s open reading frames (ORF 6 and ORF 8) produce viral proteins that specifically downregulate MHC-I molecules. All of these strategies are also exploited by other viruses to elude immune detection and should be studied in depth to improve the effectiveness of future antiviral treatments. Compared to the Wuhan strain or the Delta variant, Omicron has developed mutations that have impaired its ability to generate syncytia, thus reducing its pathogenicity. Conversely, other mutations have allowed it to escape antibody neutralization and preventing cellular immune recognition, making it the most contagious and evasive variant to date.
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Affiliation(s)
- Alberto Rubio-Casillas
- Biology Laboratory, Autlán Regional Preparatory School, University of Guadalajara, Autlán 48900, Jalisco, Mexico
- Correspondence: (A.R.-C.); (V.N.U.); Tel.: +52-317-38-935-55 (A.R.-C.)
| | - Elrashdy M. Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia;
- Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg EL-Arab, Alexandria 21934, Egypt
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Correspondence: (A.R.-C.); (V.N.U.); Tel.: +52-317-38-935-55 (A.R.-C.)
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Panico A, Lobreglio G, Bagordo F, Zizza A, De Donno A, Rosato C, Lazzari R, Chicone M, Indino F, Recchia V, Alifano P, Grassi T. Antibody Response in Healthcare Workers before and after the Third Dose of Anti-SARS-CoV-2 Vaccine: A Pilot Study. Vaccines (Basel) 2022; 10:vaccines10060862. [PMID: 35746470 PMCID: PMC9229040 DOI: 10.3390/vaccines10060862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 12/12/2022] Open
Abstract
The SARS-CoV-2 pandemic led to the development of various vaccines. The BNT162b2 mRNA vaccine was the first approved due to its efficacy in eliciting a humoral immunity response after the second dose. However, a decrease in the antibody concentration was observed over time. Therefore, the administration of a third dose was scheduled, primarily for frail people and workers of essential public activities. The aim of this study was to assess the level of antibodies against the spike (S) RBD of SARS-CoV-2 in healthcare workers before and after the third dose of BNT162b2 vaccine, according to sex, age, and the time interval between vaccine doses and tests. All 37 (12 males, 25 females, 19 < 50 years old, 18 ≥ 50 years old) healthcare workers recruited showed a consistent antibody titer increase after the third dose. Data analysis showed that the antibody concentration before the third dose significantly decreased as the time interval up to the test increased, and a significantly higher level was shown in young than older people. Cluster analysis revealed that young females had a higher antibody level than older females before the third dose (p < 0.05). This study indicated the benefit of the third dose of BNT162b2 vaccine and its effect on leveling up the humoral immune response.
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Affiliation(s)
- Alessandra Panico
- Department of Biological and Environmental Science and Technology, University of Salento, 73100 Lecce, Italy; (A.P.); (A.D.D.); (P.A.); (T.G.)
| | - Giambattista Lobreglio
- Clinical Pathology and Microbiology Unit, Vito Fazzi General Hospital, 73100 Lecce, Italy; (G.L.); (C.R.); (R.L.); (M.C.); (F.I.)
| | - Francesco Bagordo
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, 70121 Bari, Italy;
| | - Antonella Zizza
- Institute of Clinical Physiology, National Research Council, 73100 Lecce, Italy;
- Correspondence: ; Tel.: +39-0832-422306
| | - Antonella De Donno
- Department of Biological and Environmental Science and Technology, University of Salento, 73100 Lecce, Italy; (A.P.); (A.D.D.); (P.A.); (T.G.)
| | - Chiara Rosato
- Clinical Pathology and Microbiology Unit, Vito Fazzi General Hospital, 73100 Lecce, Italy; (G.L.); (C.R.); (R.L.); (M.C.); (F.I.)
| | - Roberta Lazzari
- Clinical Pathology and Microbiology Unit, Vito Fazzi General Hospital, 73100 Lecce, Italy; (G.L.); (C.R.); (R.L.); (M.C.); (F.I.)
| | - Michele Chicone
- Clinical Pathology and Microbiology Unit, Vito Fazzi General Hospital, 73100 Lecce, Italy; (G.L.); (C.R.); (R.L.); (M.C.); (F.I.)
| | - Floriano Indino
- Clinical Pathology and Microbiology Unit, Vito Fazzi General Hospital, 73100 Lecce, Italy; (G.L.); (C.R.); (R.L.); (M.C.); (F.I.)
| | - Virginia Recchia
- Institute of Clinical Physiology, National Research Council, 73100 Lecce, Italy;
| | - Pietro Alifano
- Department of Biological and Environmental Science and Technology, University of Salento, 73100 Lecce, Italy; (A.P.); (A.D.D.); (P.A.); (T.G.)
| | - Tiziana Grassi
- Department of Biological and Environmental Science and Technology, University of Salento, 73100 Lecce, Italy; (A.P.); (A.D.D.); (P.A.); (T.G.)
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