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Privitera GF, Musso N, Micale G, Bonomo C, Alaimo S, Bivona D, Bonacci PG, Scalia G, Stefani S, Pulvirenti A. CovidTGI: A tool to investigate the temporal genetic instability of SARS-CoV-2 variants. iScience 2025; 28:112315. [PMID: 40264800 PMCID: PMC12013479 DOI: 10.1016/j.isci.2025.112315] [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: 11/04/2024] [Revised: 12/21/2024] [Accepted: 03/25/2025] [Indexed: 04/24/2025] Open
Abstract
The COVID-19 pandemic has underscored the need for fast and accurate epidemiology, particularly due to the high observed mutation frequency in SARS-CoV-2. This study aims to explore the evolution of SARS-CoV-2 through a global analysis. To facilitate a comparative analysis of temporal mutation data, we developed CovidTGI, a Shiny web application. CovidTGI provides insights into observed mutation frequencies and the temporal relationships among mutations across various clades in different geographical regions. Our tool relies on a database that includes 2 million samples obtained from the National Center for Biotechnology Information (NCBI), along with 500 in-house Sicilian samples collected between May 2021 and June 2022. From this smaller group of samples, we identified key variants that are prevalent within a specific clade. Our tool is designed to study the evolution of SARS-CoV-2, which clearly follows a complex trajectory. This complexity highlights the necessity for sophisticated tools like CovidTGI to understand and track the evolution of this virus.
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Affiliation(s)
- Grete Francesca Privitera
- Department of Clinical and Experimental Medicine, Bioinformatic Unit, University of Catania, Via Santa Sofia, 95125 Catania, Italy
| | - Nicolò Musso
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Medical Molecular Microbiology and Antibiotic Resistance Laboratory (MMAR Lab), University of Catania, Via Santa Sofia, 95125 Catania, Italy
| | - Giovanni Micale
- Department of Clinical and Experimental Medicine, Bioinformatic Unit, University of Catania, Via Santa Sofia, 95125 Catania, Italy
| | - Carmelo Bonomo
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Medical Molecular Microbiology and Antibiotic Resistance Laboratory (MMAR Lab), University of Catania, Via Santa Sofia, 95125 Catania, Italy
| | - Salvatore Alaimo
- Department of Clinical and Experimental Medicine, Bioinformatic Unit, University of Catania, Via Santa Sofia, 95125 Catania, Italy
| | - Dalida Bivona
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Medical Molecular Microbiology and Antibiotic Resistance Laboratory (MMAR Lab), University of Catania, Via Santa Sofia, 95125 Catania, Italy
| | - Paolo Giuseppe Bonacci
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Medical Molecular Microbiology and Antibiotic Resistance Laboratory (MMAR Lab), University of Catania, Via Santa Sofia, 95125 Catania, Italy
| | - Guido Scalia
- U.O.C. Laboratory Analysis Unit, A.O.U. ‘Policlinico-Vittorio Emanuele’, University of Catania, Via Santa Sofia, 95125 Catania, Italy
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Medical Molecular Microbiology and Antibiotic Resistance Laboratory (MMAR Lab), University of Catania, Via Santa Sofia, 95125 Catania, Italy
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, Bioinformatic Unit, University of Catania, Via Santa Sofia, 95125 Catania, Italy
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Liu J, Li N, Wang B, Zhao W, Zhi J, Jia X, Jia Y, Tie Y. SARS-CoV-2 Infection Aggravates Physical and Mental Health in Cancer Patients Compared to Co-Living Individuals. Cancer Med 2025; 14:e70795. [PMID: 40129313 PMCID: PMC11933713 DOI: 10.1002/cam4.70795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Revised: 02/19/2025] [Accepted: 03/10/2025] [Indexed: 03/26/2025] Open
Abstract
INTRODUCTION Cancer patients are particularly vulnerable to the psychological sequels of COVID-19 due to their immunocompromised state and the disruptions to their regular oncological care. There is limited research comparing the effects of SARS-CoV-2 on cancer patients and their co-living individuals. This study aims to explore the similarities and differences in physical and psychological outcomes between these two groups, with a 1-year follow-up to assess long-term effects. METHODS This retrospective observational study was conducted between January and February 2023. A total of 107 participants were included: 72 cancer patients and 35 co-living individuals, all diagnosed with COVID-19. Clinical and laboratory data were collected. Depression, anxiety, and fatigue were assessed at two timepoints: shortly after COVID-19 diagnosis and 1 year later. RESULTS Cancer patients exhibited higher rates of gastrointestinal symptoms, such as diarrhea (20.83% vs. 5.71%, p = 0.045), which were associated with increased anxiety and depression (p < 0.05). Advanced-stage cancer (p < 0.01) and lack of vaccination (p < 0.01) correlated with worse psychological outcomes. Female cancer patients reported higher depression scores (p < 0.05). Laboratory findings indicated higher neutrophil percentages (p < 0.001), fibrinogen (p < 0.001), and D-dimer levels (p = 0.015) in cancer patients, signaling a higher risk of inflammation and thrombosis. Both groups showed improvements in depression and fatigue over the 1-year follow-up, but cancer patients continued to report greater psychological distress (p < 0.001) and fatigue (p = 0.024). CONCLUSION Cancer patients infected with COVID-19 experienced more severe physical and psychological symptoms compared to their co-living individuals, with persistent differences 1 year after infection. TRIAL REGISTRATION ChiCTR2300067577.
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Affiliation(s)
- Jiayao Liu
- The Third Department of OncologyHebei General HospitalShijiazhuangChina
- Hebei Medical UniversityShijiazhuangChina
| | - Na Li
- The Third Department of OncologyHebei General HospitalShijiazhuangChina
| | - Bin Wang
- The Third Department of OncologyHebei General HospitalShijiazhuangChina
| | - Wujie Zhao
- The Third Department of OncologyHebei General HospitalShijiazhuangChina
| | - Jie Zhi
- The Third Department of OncologyHebei General HospitalShijiazhuangChina
| | - Xiaojing Jia
- The Third Department of OncologyHebei General HospitalShijiazhuangChina
| | - Yitao Jia
- The Third Department of OncologyHebei General HospitalShijiazhuangChina
| | - Yanqing Tie
- Department of Clinical LaboratoryHebei General HospitalShijiazhuangChina
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Yang J, Wang J, Zhang H, Li S, Wang X, Baimanov D, Zhang Z, Li Y, Yu P, Zhang X, Wang L. Rapid Detection of Spike Protein Receptor Binding Region of SARS-CoV-2 and Its Variants Using a Nanosheet Probe. Anal Chem 2025; 97:3729-3738. [PMID: 39924735 DOI: 10.1021/acs.analchem.4c06613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2025]
Abstract
Strategies for the rapid detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are critically needed due to conventional methods' limitations: narrow range, virus mutation-induced failure, time-consuming, and complex operations. Herein, we propose a method utilizing CuInP2S6 nanosheet probes and Bio-Layer Interferometry (BLI) technology for the rapid (5-10 min), noninvasive, and broad-spectrum detection of the SARS-CoV-2 spike receptor binding domain (RBD) in human saliva. The nanoprobe exhibits a higher binding affinity to the RBD compared to most saliva proteins, allowing it to be immobilized on BLI sensors for easier detection of protein binding and elution. An eluent buffer containing Tween-20 and salts was employed to separate salivary proteins while retaining the RBD on the probes. This system can detect the RBD across a broad spectrum and a low limit of 25 ng/mL (S/N = 3) in less than 10 min. To validate this system, experiments with pseudoviruses showed accurate identification and binding of the RBD. Molecular dynamics simulations elucidated the mechanism for selective binding of probes to RBD. In conclusion, we propose a conceptual study based on an in situ strategy with inorganic nanoprobes alongside BLI techniques for convenient, noninvasive, and rapid detection of SARS-CoV-2 and its variants. This strategy is anticipated to inspire the design and implementation of nanoprobes for the rapid and selective detection of pathogens in the future.
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Affiliation(s)
- Jiacheng Yang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, P. R. China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Laboratory of Interface Science and Biology, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P. R. China
- Peking University Ningbo Institute of Marine Medicines, Ningbo 315832, P. R. China
| | - Heng Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Shijiao Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Laboratory of Interface Science and Biology, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xiaofeng Wang
- Laboratory of Inflammation and Vaccines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, Guangdong, P. R. China
| | - Didar Baimanov
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Laboratory of Interface Science and Biology, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Zehao Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Laboratory of Interface Science and Biology, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yang Li
- Laboratory of Inflammation and Vaccines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, Guangdong, P. R. China
| | - Peng Yu
- School of Materials Science and Engineering, Sun Yat-sen University, Guangzhou 510275, Guangdong, P. R. China
| | - Xinfeng Zhang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, P. R. China
| | - Liming Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Laboratory of Interface Science and Biology, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, P. R. China
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Medeiros-Silva J, Pankratova Y, Sučec I, Dregni AJ, Hong M. Polar Networks Mediate Ion Conduction of the SARS-CoV-2 Envelope Protein. J Am Chem Soc 2025; 147:746-757. [PMID: 39726395 DOI: 10.1021/jacs.4c13229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2024]
Abstract
The SARS-CoV-2 E protein conducts cations across the cell membrane to cause pathogenicity to infected cells. The high-resolution structures of the E transmembrane domain (ETM) in the closed state at neutral pH and in the open state at acidic pH have been determined. However, the ion conduction mechanism remains elusive. Here, we use solid-state NMR spectroscopy to investigate the side chain structure, dynamics, and interactions of five polar residues at the N-terminal entrance of the channel and three polar residues at the C-terminal end. The chemical shifts of the N-terminal Glu8 reveal that the Glu side chain interacts with protons, Ca2+ and two neighboring Thr residues, and adopts distinct motionally averaged conformational ensembles. These polar interactions are sensitive to the presence of negatively charged lipids in the membrane. A T9I mutation, prevalent in the Omicron variants of SARS-CoV-2 E, perturbs these interactions and partially immobilizes the N-terminal segment. Deeper into the channel, two polar residues, Asn15 and Ser16, form interhelical hydrogen bonds in the closed state but become separated by water molecules in the open state. This is manifested by Asn15-Ser16 correlation signals at neutral pH and the loss of these correlations and the appearance of water cross peaks with Ser16 at acidic pH in the presence of Ca2+. Finally, the guanidinium side chain of the C-terminal Arg38 undergoes fast reorientations in the closed state but becomes more restricted in the open state. These results provide evidence for a dynamic and hydrogen-bonded N-terminal polar network that recruits and relays protons and Ca2+ in a lipid-dependent manner. Once inside, the ions permeate past the hydrophobic middle of the transmembrane domain with the help of enhanced hydrophilicity of the C-terminal channel lumen due to the insertion of the Arg38 side chain into the pore.
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Affiliation(s)
- João Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Yanina Pankratova
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Iva Sučec
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Aurelio J Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
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5
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Wasim R, Sumaiya, Ahmad A. Across-the-board review on Omicron SARS-CoV-2 variant. Inflammopharmacology 2025; 33:1-10. [PMID: 39714724 DOI: 10.1007/s10787-024-01627-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2024] [Accepted: 12/07/2024] [Indexed: 12/24/2024]
Abstract
INTRODUCTION Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in a cataclysmic pandemic. Several SARS-CoV-2 mutations have been found and reported since the COVID-19 pandemic began. After the Alpha, Beta, Gamma, and Delta variants, the Omicron (B.1.1.529) is the most recently emerged variant of concern (VOC), which has evolved as a result of a high number of mutations, particularly in the spike protein, raising concerns about its ability to evade pre-existing immunity acquired through vaccination or natural infection. METHODS This is a review based on studies published from November 2021 to September 2024. RESULT AND DISCUSSIONS The current article discusses the advent of the SARS-CoV-2 Omicron variant, its key characteristics and significant global health concerns, as well as measures for dealing with it in the context of the continuing COVID-19 pandemic. Various mutations in Omicron have been discussed that contribute to increased transmissibility and immune evasion from vaccine-induced or natural immunity acquired after infection. To understand the similarities and differences between different VOCs and Omicron, we conducted a comparative investigation. CONCLUSION Strengthening research, improving genomic surveillance and tracking, developing highly effective vaccines and immunotherapies, designing appropriate strategies, action plans, and future preparedness plans must all be prioritized and implemented quickly at global levels to mitigate the high global health concerns associated with the emergence of this new Omicron variant well before it causes large-scale COVID-19 outbreaks.
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Affiliation(s)
- Rufaida Wasim
- Department of Pharmacy, Integral University, Lucknow, 226026, India.
| | - Sumaiya
- Career Post Graduate Institute of Dental Sciences and Hospital, Lucknow, India
| | - Asad Ahmad
- Department of Pharmacy, Integral University, Lucknow, 226026, India
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6
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Carvajal-Rodríguez A. iHDSel software: The price equation and the population stability index to detect genomic patterns compatible with selective sweeps. An example with SARS-CoV-2. Biol Methods Protoc 2024; 9:bpae089. [PMID: 39679303 PMCID: PMC11646571 DOI: 10.1093/biomethods/bpae089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2024] [Revised: 11/19/2024] [Accepted: 11/25/2024] [Indexed: 12/17/2024] Open
Abstract
A large number of methods have been developed and continue to evolve for detecting the signatures of selective sweeps in genomes. Significant advances have been made, including the combination of different statistical strategies and the incorporation of artificial intelligence (machine learning) methods. Despite these advances, several common problems persist, such as the unknown null distribution of the statistics used, necessitating simulations and resampling to assign significance to the statistics. Additionally, it is not always clear how deviations from the specific assumptions of each method might affect the results. In this work, allelic classes of haplotypes are used along with the informational interpretation of the Price equation to design a statistic with a known distribution that can detect genomic patterns caused by selective sweeps. The statistic consists of Jeffreys divergence, also known as the population stability index, applied to the distribution of allelic classes of haplotypes in two samples. Results with simulated data show optimal performance of the statistic in detecting divergent selection. Analysis of real severe acute respiratory syndrome coronavirus 2 genome data also shows that some of the sites playing key roles in the virus's fitness and immune escape capability are detected by the method. The new statistic, called JHAC , is incorporated into the iHDSel (informed HacDivSel) software available at https://acraaj.webs.uvigo.es/iHDSel.html.
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Affiliation(s)
- Antonio Carvajal-Rodríguez
- Centro de Investigación Mariña (CIM), Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, 36310 Spain
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Ramos BD, Hudson NR, Gonzales DE, Brown AN, White MG, Browde RJ, McNeary-Garvin AM, Knight CE, Pham KC, Sweatt RJ, Phan LM, Ly E, Garcia AR. Evaluation of Self-collected Saliva Samples Without Viral Transport Media for SARS-CoV-2 Testing via RT-PCR and Comparison of Amplicon Sequences Against Commonly Used Primers in Diagnostic Assays. Mil Med 2024; 189:184-189. [PMID: 39160794 DOI: 10.1093/milmed/usae070] [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: 11/24/2023] [Revised: 01/26/2024] [Accepted: 02/16/2024] [Indexed: 08/21/2024] Open
Abstract
INTRODUCTION Mass screening for SARS-CoV-2 using nasopharyngeal swabs (NPS) is costly, uncomfortable for patients, and increases the chance of virus exposure to health care workers. Therefore, this study focused on determining if self-collected unpreserved saliva can be an effective alternative to NPS collection in COVID-19 surveillance. MATERIALS AND METHODS In this study, patients being tested for SARS-CoV-2 using NPS were asked to provide a saliva sample to compare their results. NPS samples were evaluated for SARS-CoV-2 using BioFire® FilmArray® Torch® or Cepheid® GeneXpert® systems while saliva samples were evaluated using an in-house developed reverse transcriptase polymerase chain reaction (RT-PCR) which targeted the Envelope (E) and Nucleocapsid (N) genes. RESULTS Detection of SARS-CoV-2 using self-collected saliva was found to be only slightly less accurate (<5%) than testing using NPS. In addition, initial saliva RT-PCR identified 27 positive subjects, 18 of which provided amplicons sufficient for confirmatory sequencing. The sequencing data showed a genetic shift in the virus within our population sometime between 22 June and July 8, 2021 from Alpha to Delta variant. CONCLUSIONS The saliva sample collection method identifies the E gene in SARS COVID-2 samples which provides an alternative specimen source to the NPS. This identifies the S gene and ORF1ab. Saliva collection is more convenient to the patient, yields comparable results to NPS collection, and potentially increases Covid-19 surveillance.
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Affiliation(s)
- Benjamin D Ramos
- Department of Pathology, 60th Medical Group (MDG), Travis Air Force Base (AFB), Fairfield, CA 94535, USA
| | - N Ryan Hudson
- Clinical Investigation Facility, 60MDG, Fairfield, CA 94535, USA
| | - Diane E Gonzales
- Clinical Investigation Facility, 60MDG, Fairfield, CA 94535, USA
| | - Ashleigh N Brown
- Clinical Investigation Facility, 60MDG, Fairfield, CA 94535, USA
| | - Matthew G White
- Clinical Investigation Facility, 60MDG, Fairfield, CA 94535, USA
| | - Ryan J Browde
- Clinical Investigation Facility, 60MDG, Fairfield, CA 94535, USA
| | | | - Celynn E Knight
- Clinical Investigation Facility, 60MDG, Fairfield, CA 94535, USA
| | - Kevin C Pham
- Clinical Investigation Facility, 60MDG, Fairfield, CA 94535, USA
| | - Robert J Sweatt
- Clinical Investigation Facility, 60MDG, Fairfield, CA 94535, USA
| | - Liem Minh Phan
- Clinical Investigation Facility, 60MDG, Fairfield, CA 94535, USA
| | - Eileen Ly
- Clinical Investigation Facility, 60MDG, Fairfield, CA 94535, USA
| | - Andrew R Garcia
- Clinical Investigation Facility, 60MDG, Fairfield, CA 94535, USA
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Rajaiah R, Pandey K, Acharya A, Ambikan A, Kumar N, Guda R, Avedissian SN, Montaner LJ, Cohen SM, Neogi U, Byrareddy SN. Differential immunometabolic responses to Delta and Omicron SARS-CoV-2 variants in golden syrian hamsters. iScience 2024; 27:110501. [PMID: 39171289 PMCID: PMC11338146 DOI: 10.1016/j.isci.2024.110501] [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: 08/24/2023] [Revised: 02/07/2024] [Accepted: 07/10/2024] [Indexed: 08/23/2024] Open
Abstract
Delta (B.1.617.2) and Omicron (B.1.1.529) variants of SARS-CoV-2 represents unique clinical characteristics. However, their role in altering immunometabolic regulations during acute infection remains convoluted. Here, we evaluated the differential immunopathogenesis of Delta vs. Omicron variants in Golden Syrian hamsters (GSH). The Delta variant resulted in higher virus titers in throat swabs and the lungs and exhibited higher lung damage with immune cell infiltration than the Omicron variant. The gene expression levels of immune mediators and metabolic enzymes, Arg-1 and IDO1 in the Delta-infected lungs were significantly higher compared to Omicron. Further, Delta/Omicron infection perturbed carbohydrates, amino acids, nucleotides, and TCA cycle metabolites and was differentially regulated compared to uninfected lungs. Collectively, our data provide a novel insight into immunometabolic/pathogenic outcomes for Delta vs. Omicron infection in the GSH displaying concordance with COVID-19 patients associated with inflammation and tissue injury during acute infection that offered possible new targets to develop potential therapeutics.
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Affiliation(s)
- Rajesh Rajaiah
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Kabita Pandey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Anoop Ambikan
- The Systems Virology Lab, Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, 141 52 Stockholm, Sweden
| | - Narendra Kumar
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Reema Guda
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Sean N. Avedissian
- Antiviral Pharmacology Laboratory, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Luis J. Montaner
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Samuel M. Cohen
- Havlik Wall Professor of Oncology, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ujjwal Neogi
- The Systems Virology Lab, Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, 141 52 Stockholm, Sweden
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
- Havlik Wall Professor of Oncology, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
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Redd PS, Merting AD, Klement JD, Poschel DB, Yang D, Liu K. In vitro antibody-mediated SARS-CoV-2 infection suppression through human ACE2 receptor blockade. Immunol Lett 2024; 268:106887. [PMID: 38925442 PMCID: PMC11256821 DOI: 10.1016/j.imlet.2024.106887] [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: 02/26/2024] [Revised: 05/23/2024] [Accepted: 06/22/2024] [Indexed: 06/28/2024]
Abstract
Vaccines and antibodies that specifically target or neutralize components of the SARS-CoV-2 virus are effective in prevention and treatment of human patients with SARS-CoV-2 infection. However, vaccines and SARS-CoV-2 neutralization antibodies target a subset of epitopes of viral proteins, and the fast evolution of the SARS-CoV-2 virus and the continuing emergence of SARS-CoV-2 variants confer SARS-CoV-2 immune escape from these therapies. ACE2 is the human cell receptor that serves as the entry point for SARS-CoV-2 into human cells and thus is the gatekeeper for SARS-CoV-2 infection of humans. We report here the development of 4G8C11, an anti-human ACE2 receptor monoclonal antibody that recognizes ACE2 on human cell surfaces. We determined that 4G8C11 blocks SARS-CoV-2 and variant infection of ACE2+ human cells. Furthermore, 4G8C11 has minimal effects on ACE2 receptor activity. 4G8C11 is therefore a monoclonal antibody for ACE2 receptor detection and potentially an effective immunotherapeutic agent for SARS-CoV-2 and variants.
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Affiliation(s)
- Priscilla S Redd
- CheMedImmune Inc., Augusta, GA 30912, USA; Department of Biochemistry and Molecular Biology, Medical College of Georgia. Augusta, GA 30912, USA; Georgia Cancer Center, Augusta, GA 30912, USA; Charlie Norwood VA Medical Center, Augusta, GA 30904, USA.
| | - Alyssa D Merting
- Department of Biochemistry and Molecular Biology, Medical College of Georgia. Augusta, GA 30912, USA; Georgia Cancer Center, Augusta, GA 30912, USA; Charlie Norwood VA Medical Center, Augusta, GA 30904, USA
| | - John D Klement
- Department of Biochemistry and Molecular Biology, Medical College of Georgia. Augusta, GA 30912, USA; Georgia Cancer Center, Augusta, GA 30912, USA; Charlie Norwood VA Medical Center, Augusta, GA 30904, USA
| | - Dakota B Poschel
- Department of Biochemistry and Molecular Biology, Medical College of Georgia. Augusta, GA 30912, USA; Georgia Cancer Center, Augusta, GA 30912, USA; Charlie Norwood VA Medical Center, Augusta, GA 30904, USA
| | - Dafeng Yang
- Department of Biochemistry and Molecular Biology, Medical College of Georgia. Augusta, GA 30912, USA; Georgia Cancer Center, Augusta, GA 30912, USA; Charlie Norwood VA Medical Center, Augusta, GA 30904, USA
| | - Kebin Liu
- Department of Biochemistry and Molecular Biology, Medical College of Georgia. Augusta, GA 30912, USA; Georgia Cancer Center, Augusta, GA 30912, USA; Charlie Norwood VA Medical Center, Augusta, GA 30904, USA
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Hu WH, Cai HL, Yan HC, Wang H, Sun HM, Wei YY, Hao YT. Protective effectiveness of previous infection against subsequent SARS-Cov-2 infection: systematic review and meta-analysis. Front Public Health 2024; 12:1353415. [PMID: 38966699 PMCID: PMC11222391 DOI: 10.3389/fpubh.2024.1353415] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 06/04/2024] [Indexed: 07/06/2024] Open
Abstract
Background The protective effectiveness provided by naturally acquired immunity against SARS-CoV-2 reinfection remain controversial. Objective To systematically evaluate the protective effect of natural immunity against subsequent SARS-CoV-2 infection with different variants. Methods We searched for related studies published in seven databases before March 5, 2023. Eligible studies included in the analysis reported the risk of subsequent infection for groups with or without a prior SARS-CoV-2 infection. The primary outcome was the overall pooled incidence rate ratio (IRR) of SARS-CoV-2 reinfection/infection between the two groups. We also focused on the protective effectiveness of natural immunity against reinfection/infection with different SARS-CoV-2 variants. We used a random-effects model to pool the data, and obtained the bias-adjusted results using the trim-and-fill method. Meta-regression and subgroup analyses were conducted to explore the sources of heterogeneity. Sensitivity analysis was performed by excluding included studies one by one to evaluate the stability of the results. Results We identified 40 eligible articles including more than 20 million individuals without the history of SARS-CoV-2 vaccination. The bias-adjusted efficacy of naturally acquired antibodies against reinfection was estimated at 65% (pooled IRR = 0.35, 95% CI = 0.26-0.47), with higher efficacy against symptomatic COVID-19 cases (pooled IRR = 0.15, 95% CI = 0.08-0.26) than asymptomatic infection (pooled IRR = 0.40, 95% CI = 0.29-0.54). Meta-regression revealed that SARS-CoV-2 variant was a statistically significant effect modifier, which explaining 46.40% of the variation in IRRs. For different SARS-CoV-2 variant, the pooled IRRs for the Alpha (pooled IRR = 0.11, 95% CI = 0.06-0.19), Delta (pooled IRR = 0.19, 95% CI = 0.15-0.24) and Omicron (pooled IRR = 0.61, 95% CI = 0.42-0.87) variant were higher and higher. In other subgroup analyses, the pooled IRRs of SARS-CoV-2 infection were statistically various in different countries, publication year and the inclusion end time of population, with a significant difference (p = 0.02, p < 0.010 and p < 0.010), respectively. The risk of subsequent infection in the seropositive population appeared to increase slowly over time. Despite the heterogeneity in included studies, sensitivity analyses showed stable results. Conclusion Previous SARS-CoV-2 infection provides protection against pre-omicron reinfection, but less against omicron. Ongoing viral mutation requires attention and prevention strategies, such as vaccine catch-up, in conjunction with multiple factors.
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Affiliation(s)
- Wei-Hua Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing, China
| | - Huan-Le Cai
- Department of Medical Statistics, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Huan-Chang Yan
- Department of Medical Statistics, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Han Wang
- Department of Medical Statistics, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Hui-Min Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing, China
| | - Yong-Yue Wei
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing, China
| | - Yuan-Tao Hao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing, China
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11
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Li X, Mi Z, Liu Z, Rong P. SARS-CoV-2: pathogenesis, therapeutics, variants, and vaccines. Front Microbiol 2024; 15:1334152. [PMID: 38939189 PMCID: PMC11208693 DOI: 10.3389/fmicb.2024.1334152] [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: 11/06/2023] [Accepted: 05/29/2024] [Indexed: 06/29/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in December 2019 with staggering economic fallout and human suffering. The unique structure of SARS-CoV-2 and its underlying pathogenic mechanism were responsible for the global pandemic. In addition to the direct damage caused by the virus, SARS-CoV-2 triggers an abnormal immune response leading to a cytokine storm, culminating in acute respiratory distress syndrome and other fatal diseases that pose a significant challenge to clinicians. Therefore, potential treatments should focus not only on eliminating the virus but also on alleviating or controlling acute immune/inflammatory responses. Current management strategies for COVID-19 include preventative measures and supportive care, while the role of the host immune/inflammatory response in disease progression has largely been overlooked. Understanding the interaction between SARS-CoV-2 and its receptors, as well as the underlying pathogenesis, has proven to be helpful for disease prevention, early recognition of disease progression, vaccine development, and interventions aimed at reducing immunopathology have been shown to reduce adverse clinical outcomes and improve prognosis. Moreover, several key mutations in the SARS-CoV-2 genome sequence result in an enhanced binding affinity to the host cell receptor, or produce immune escape, leading to either increased virus transmissibility or virulence of variants that carry these mutations. This review characterizes the structural features of SARS-CoV-2, its variants, and their interaction with the immune system, emphasizing the role of dysfunctional immune responses and cytokine storm in disease progression. Additionally, potential therapeutic options are reviewed, providing critical insights into disease management, exploring effective approaches to deal with the public health crises caused by SARS-CoV-2.
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Affiliation(s)
- Xi Li
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ze Mi
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhenguo Liu
- Department of Infectious Disease, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Pengfei Rong
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, China
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12
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Carvajal JJ, García-Castillo V, Cuellar SV, Campillay-Véliz CP, Salazar-Ardiles C, Avellaneda AM, Muñoz CA, Retamal-Díaz A, Bueno SM, González PA, Kalergis AM, Lay MK. New insights into the pathogenesis of SARS-CoV-2 during and after the COVID-19 pandemic. Front Immunol 2024; 15:1363572. [PMID: 38911850 PMCID: PMC11190347 DOI: 10.3389/fimmu.2024.1363572] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 04/24/2024] [Indexed: 06/25/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the respiratory distress condition known as COVID-19. This disease broadly affects several physiological systems, including the gastrointestinal, renal, and central nervous (CNS) systems, significantly influencing the patient's overall quality of life. Additionally, numerous risk factors have been suggested, including gender, body weight, age, metabolic status, renal health, preexisting cardiomyopathies, and inflammatory conditions. Despite advances in understanding the genome and pathophysiological ramifications of COVID-19, its precise origins remain elusive. SARS-CoV-2 interacts with a receptor-binding domain within angiotensin-converting enzyme 2 (ACE2). This receptor is expressed in various organs of different species, including humans, with different abundance. Although COVID-19 has multiorgan manifestations, the main pathologies occur in the lung, including pulmonary fibrosis, respiratory failure, pulmonary embolism, and secondary bacterial pneumonia. In the post-COVID-19 period, different sequelae may occur, which may have various causes, including the direct action of the virus, alteration of the immune response, and metabolic alterations during infection, among others. Recognizing the serious adverse health effects associated with COVID-19, it becomes imperative to comprehensively elucidate and discuss the existing evidence surrounding this viral infection, including those related to the pathophysiological effects of the disease and the subsequent consequences. This review aims to contribute to a comprehensive understanding of the impact of COVID-19 and its long-term effects on human health.
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Affiliation(s)
- Jonatan J. Carvajal
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | - Valeria García-Castillo
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | - Shelsy V. Cuellar
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | | | - Camila Salazar-Ardiles
- Center for Research in Physiology and Altitude Medicine (FIMEDALT), Biomedical Department, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Andrea M. Avellaneda
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Department of Basic Sciences, Faculty of Sciences, Universidad Santo Tomás, Antofagasta, Chile
| | - Christian A. Muñoz
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Angello Retamal-Díaz
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Susan M. Bueno
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo A. González
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexis M. Kalergis
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Margarita K. Lay
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
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13
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Kircheis R. In Silico Analyses Indicate a Lower Potency for Dimerization of TLR4/MD-2 as the Reason for the Lower Pathogenicity of Omicron Compared to Wild-Type Virus and Earlier SARS-CoV-2 Variants. Int J Mol Sci 2024; 25:5451. [PMID: 38791489 PMCID: PMC11121871 DOI: 10.3390/ijms25105451] [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: 03/27/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
The SARS-CoV-2 Omicron variants have replaced all earlier variants, due to increased infectivity and effective evasion from infection- and vaccination-induced neutralizing antibodies. Compared to earlier variants of concern (VoCs), the Omicron variants show high TMPRSS2-independent replication in the upper airway organs, but lower replication in the lungs and lower mortality rates. The shift in cellular tropism and towards lower pathogenicity of Omicron was hypothesized to correlate with a lower toll-like receptor (TLR) activation, although the underlying molecular mechanisms remained undefined. In silico analyses presented here indicate that the Omicron spike protein has a lower potency to induce dimerization of TLR4/MD-2 compared to wild type virus despite a comparable binding activity to TLR4. A model illustrating the molecular consequences of the different potencies of the Omicron spike protein vs. wild-type spike protein for TLR4 activation is presented. Further analyses indicate a clear tendency for decreasing TLR4 dimerization potential during SARS-CoV-2 evolution via Alpha to Gamma to Delta to Omicron variants.
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14
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Le HT, Tran LH, Phung HTT. SARS-CoV-2 omicron RBD forms a weaker binding affinity to hACE2 compared to Delta RBD in in-silico studies. J Biomol Struct Dyn 2024; 42:4087-4096. [PMID: 37345564 DOI: 10.1080/07391102.2023.2222827] [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: 03/22/2023] [Accepted: 05/21/2023] [Indexed: 06/23/2023]
Abstract
The COVID-19 pandemic sparked an unprecedented race in biotechnology in a search for effective therapies and a preventive vaccine. The continued appearance of SARS-CoV-2 variants of concern (VoCs) further swept the world. The entry of SARS-CoV-2 into cells is mediated by binding the receptor-binding domain (RBD) of the S protein to the cell-surface receptor, human angiotensin-converting enzyme 2 (hACE2). In this study, using a coarse-grained force field to parameterize the system, we employed steered-molecular dynamics (SMD) simulations to reveal the binding of SARS-CoV-2 Delta/Omicron RBD to hACE2. Our benchmarked results demonstrate a good correlation between computed rupture force and experimental binding free energy for known protein-protein systems. Moreover, our findings show that the Omicron RBD has a weaker binding affinity to hACE2, consistent with the respective experimental results. This indicates that our method can effectively be applied to other emerging SARS-CoV-2 strains.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hoa Thanh Le
- Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Linh Hoang Tran
- Faculty of Civil Engineering, Ho Chi Minh City University of Technology (HCMUT), Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
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15
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Glenet M, Lebreil AL, N'Guyen Y, Meyer I, Baud S, Andreoletti L. Structural impact of a new spike Y170W mutation detected in early emerging SARS-CoV-2 Omicron variants in France. Virus Res 2024; 343:199354. [PMID: 38492859 PMCID: PMC10957500 DOI: 10.1016/j.virusres.2024.199354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
To assess the genetic characteristics of the early emerging SARS-CoV-2 Omicron variant strains, we retrospectively analyzed a collection of 150 nasopharyngeal samples taken from a series of outpatient cases tested positive by a referenced qRT-PCR assay during the reported period of Omicron variant emergence in December 2021, in northeastern region of France. Next Generation Sequencing (NGS) analysis of SARS-CoV-2 spike sequences revealed that only 3 (2 %) of these detected strains were Omicron variants, while 147 (98 %) were identified as previously described delta variants. Our phylogenetic analyzes of SARS-CoV-2 RNA genomes showed that these French early emerging Omicron variants may have originated from South Africa or India. In addition, whole viral genome sequences NGS comparison analyzes allowed us to identify an original and uncharacterized Y170W spike mutation that was weakly and transiently detected during the period of SARS-CoV-2 Omicron variant emergence in human populations. Molecular modeling and docking experiments indicated that this original mutated residue Y170W was neither directly involved in binding to the SARS-CoV-2 receptor ACE2 nor in interacting with known neutralizing antibody sites. However, this new mutation may be responsible for preventing the transition from the closed to the open Spike conformation, thus promoting the early emergence of the Omicron variant. Overall, these results underscore the epidemiological utility of a routine whole-genome viral NGS strategy that enables genotypic characterization of emerging or mutant SARS-CoV-2 variants, which could have significant implications for public health policy.
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Affiliation(s)
- Marie Glenet
- University of Reims Champagne-Ardenne, Laboratory of Virology, CardioVir UMR-S 1320 51 rue Cognacq Jay, REIMS Cedex, Reims 51092, France.
| | - Anne-Laure Lebreil
- University of Reims Champagne-Ardenne, Laboratory of Virology, CardioVir UMR-S 1320 51 rue Cognacq Jay, REIMS Cedex, Reims 51092, France
| | - Yohan N'Guyen
- University of Reims Champagne-Ardenne, Laboratory of Virology, CardioVir UMR-S 1320 51 rue Cognacq Jay, REIMS Cedex, Reims 51092, France; Infectious Diseases and Internal Medicine Department, CHU Reims, Hôpital Robert Debré, Reims, France
| | - Ittah Meyer
- Unilabs BioCT, Private Laboratory Group, Château-Thierry, France
| | - Stéphanie Baud
- Université de Reims Champagne-Ardenne, CNRS, MEDyC UMR 7369, Reims, France
| | - Laurent Andreoletti
- University of Reims Champagne-Ardenne, Laboratory of Virology, CardioVir UMR-S 1320 51 rue Cognacq Jay, REIMS Cedex, Reims 51092, France; Virology Department, CHU Reims, Hôpital Robert Debré, Reims, France
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16
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Senevirathne TH, Wekking D, Swain JWR, Solinas C, De Silva P. COVID-19: From emerging variants to vaccination. Cytokine Growth Factor Rev 2024; 76:127-141. [PMID: 38135574 DOI: 10.1016/j.cytogfr.2023.11.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023]
Abstract
The vigorous spread of SARS-CoV-2 resulted in the rapid infection of millions of people worldwide and devastation of not only public healthcare, but also social, educational, and economic infrastructures. The evolution of SARS-CoV-2 over time is due to the mutations that occurred in the genome during each replication. These mutated forms of SARS-CoV-2, otherwise known as variants, were categorized as variants of interest (VOI) or variants of concern (VOC) based on the increased risk of transmissibility, disease severity, immune escape, decreased effectiveness of current social measures, and available vaccines and therapeutics. The swift development of COVID-19 vaccines has been a great success for biomedical research, and billions of vaccine doses, including boosters, have been administered worldwide. BNT162b2 vaccine (Pfizer-BioNTech), mRNA-1273 (Moderna), ChAdOx1 nCoV-19 (AstraZeneca), and Janssen (Johnson & Johnson) are the four major COVID-19 vaccines that received early regulatory authorization based on their efficacy. However, some SARS-CoV-2 variants resulted in higher resistance to available vaccines or treatments. It has been four years since the first reported infection of SARS-CoV-2, yet the Omicron variant and its subvariants are still infecting people worldwide. Despite this, COVID-19 vaccines are still expected to be effective at preventing severe disease, hospitalization, and death from COVID. In this review, we provide a comprehensive overview of the COVID-19 pandemic focused on evolution of VOC and vaccination strategies against them.
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Affiliation(s)
- Thilini H Senevirathne
- Faculty of Science, Katholieke Universiteit Leuven, Kasteelpark Arenberg, Leuven, Belgium
| | - Demi Wekking
- Amsterdam UMC, Location Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Cinzia Solinas
- Medical Oncology, AOU Cagliari, P.O. Duilio Casula, Monserrato (CA), Italy.
| | - Pushpamali De Silva
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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17
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Ghosh AK, Yadav M, Iddum S, Ghazi S, Lendy EK, Jayashankar U, Beechboard SN, Takamatsu Y, Hattori SI, Amano M, Higashi-Kuwata N, Mitsuya H, Mesecar AD. Exploration of P1 and P4 modifications of nirmatrelvir: Design, synthesis, biological evaluation, and X-ray structural studies of SARS-CoV-2 Mpro inhibitors. Eur J Med Chem 2024; 267:116132. [PMID: 38335815 PMCID: PMC10964431 DOI: 10.1016/j.ejmech.2024.116132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 02/12/2024]
Abstract
We report the synthesis, biological evaluation, and X-ray structural studies of a series of SARS-CoV-2 Mpro inhibitors based upon the X-ray crystal structure of nirmatrelvir, an FDA approved drug that targets the main protease of SARS-CoV-2. The studies involved examination of various P4 moieties, P1 five- and six-membered lactam rings to improve potency. In particular, the six-membered P1 lactam ring analogs exhibited high SARS-CoV-2 Mpro inhibitory activity. Several compounds effectively blocked SARS-CoV-2 replication in VeroE6 cells. One of these compounds maintained good antiviral activity against variants of concern including Delta and Omicron variants. A high-resolution X-ray crystal structure of an inhibitor bound to SARS-CoV-2 Mpro was determined to gain insight into the ligand-binding properties in the Mpro active site.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA; Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA.
| | - Monika Yadav
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Satyanarayana Iddum
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Somayeh Ghazi
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Emma K Lendy
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Uttara Jayashankar
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Sydney N Beechboard
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Yuki Takamatsu
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo, 162-8655, Japan
| | - Shin-Ichiro Hattori
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo, 162-8655, Japan
| | - Masayuki Amano
- Department of Clinical Retrovirology, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Nobuyo Higashi-Kuwata
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo, 162-8655, Japan
| | - Hiroaki Mitsuya
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo, 162-8655, Japan; Department of Infectious Diseases, Kumamoto University School of Medicine, Kumamoto, 860-8556, Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch National Cancer Institute, Bethesda, MD, 20892, USA
| | - Andrew D Mesecar
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA; Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA; Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
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18
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Chakraborty C, Mallick B, Bhattacharya M, Byrareddy SN. SARS-CoV-2 Omicron Spike shows strong binding affinity and favourable interaction landscape with the TLR4/MD2 compared to other variants. J Genet Eng Biotechnol 2024; 22:100347. [PMID: 38494253 PMCID: PMC10980867 DOI: 10.1016/j.jgeb.2023.100347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 12/06/2023] [Indexed: 03/19/2024]
Abstract
Emergences of SARS-CoV-2 variants have made the pandemic more critical. Toll-like receptor 4 (TLR4) recognizes the molecular patterns of pathogens and activates the production of proinflammatory cytokines to restrain the infection. We have identified a molecular basis of interaction between the Spike and TLR4 of SARS-CoV-2 and its present and past VOCs (variant- of concern) through in silico analysis. The interaction of wild type Spike with TLR4 showed 15 number hydrogen bonds formation. Similarly, the Alpha variants' Spike with the TLR4 has illustrated that 14 hydrogen bonds participated in the interaction. However, the Delta Spike and TLR4 interaction interface showed that 17 hydrogen bonds were formed during the interaction. Furthermore, Omicron S-glycoprotein and TLR4 interaction interface was depicted (interaction score: -170.3), and 16 hydrogen bonds were found to have been formed in the interaction. Omicron S-glycoprotein shows stronger binding affinity with the TLR4 than wild type, Alpha, and Delta variants. Similarly, the Alpha Spike shows higher binding affinity with TLR4 than the wild type and Delta variant. Now, it is an open question of the molecular basis of the interaction of Spike and TLR4 and the activated downstream signaling events of TLR4 for SARS-CoV-2 and its variants.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India.
| | - Bidyut Mallick
- Department of Applied Sciences and Humanities, Galgotias College of Engineering and Technology, Knowledge Park-II, Greater Noida 201306, India
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience Durham Research Center, 8047 985880 Nebraska Medical Center Omaha, NE 68198-5880, USA.
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19
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Selvavinayagam ST, Suvaithenamudhan S, Yong YK, Hemashree K, Rajeshkumar M, Kumaresan A, Arthydevi P, Kannan M, Gopalan N, Vignesh R, Murugesan A, Sivasankaran MP, Sankar S, Cheedarla N, Anshad AR, Govindaraj S, Zhang Y, Tan HY, Larsson M, Saravanan S, Balakrishnan P, Kulanthaivel L, Singh K, Joseph N, Velu V, Byrareddy SN, Shankar EM, Raju S. Genomic surveillance of omicron B.1.1.529 SARS-CoV-2 and its variants between December 2021 and March 2023 in Tamil Nadu, India-A state-wide prospective longitudinal study. J Med Virol 2024; 96:e29456. [PMID: 38329187 DOI: 10.1002/jmv.29456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/10/2024] [Accepted: 01/23/2024] [Indexed: 02/09/2024]
Abstract
A state-wide prospective longitudinal investigation of the genomic surveillance of the omicron B.1.1.529 SARS-CoV-2 variant and its sublineages in Tamil Nadu, India, was conducted between December 2021 and March 2023. The study aimed to elucidate their mutational patterns and their genetic interrelationship in the Indian population. The study identified several unique mutations at different time-points, which likely could attribute to the changing disease characteristics, transmission, and pathogenicity attributes of omicron variants. The study found that the omicron variant is highly competent in its mutating potentials, and that it continues to evolve in the general population, likely escaping from natural as well as vaccine-induced immune responses. Our findings suggest that continuous surveillance of viral variants at the global scenario is warranted to undertake intervention measures against potentially precarious SARS-CoV-2 variants and their evolution.
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Affiliation(s)
- Sivaprakasam T Selvavinayagam
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu, India
| | - Suvaiyarasan Suvaithenamudhan
- Infection and Inflammation, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
- School of Biomedical Sciences, Sri Balaji Vidyapeeth, (Deemed to be University), Pondicherry, India
| | - Yean K Yong
- Laboratory Centre, Xiamen University Malaysia, Sepang, Selangor, Malaysia
- Kelip-kelip! Center of Excellence for Light Enabling Technologies, Xiamen University Malaysia, Sepang, Selangor, Malaysia
| | - Kannan Hemashree
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu, India
| | - Manivannan Rajeshkumar
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu, India
| | - Anandhazhvar Kumaresan
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu, India
| | - Parthiban Arthydevi
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu, India
| | - Meganathan Kannan
- Blood and Vascular Biology, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| | - Natarajan Gopalan
- Department of Epidemiology and Public Health, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| | - Ramachandran Vignesh
- Preclinical Department, Faculty of Medicine, Royal College of Medicine Perak, Universiti Kuala Lumpur, Ipoh, Perak, Malaysia
| | - Amudhan Murugesan
- Department of Microbiology, The Government Theni Medical College and Hospital, Theni, Tamil Nadu, India
| | | | - Sathish Sankar
- Department of Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Science, Chennai, Tamil Nadu, India
| | - Narayanaiah Cheedarla
- Division of Microbiology and Immunology, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Emory National Primate Research Center, Emory Vaccine Center, Atlanta, Georgia, USA
| | - Abdul R Anshad
- Infection and Inflammation, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| | - Sakthivel Govindaraj
- Division of Microbiology and Immunology, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Emory National Primate Research Center, Emory Vaccine Center, Atlanta, Georgia, USA
| | - Ying Zhang
- Kelip-kelip! Center of Excellence for Light Enabling Technologies, Xiamen University Malaysia, Sepang, Selangor, Malaysia
- Chemical Engineering, Xiamen University Malaysia, Sepang, Malaysia
| | - Hong Y Tan
- Laboratory Centre, Xiamen University Malaysia, Sepang, Selangor, Malaysia
- School of Traditional Chinese Medicine, Xiamen University Malaysia, Sepang, Malaysia
| | - Marie Larsson
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Shanmugam Saravanan
- Center for Infectious Diseases, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, India
| | - Pachamuthu Balakrishnan
- Center for Infectious Diseases, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, India
| | - Langeswaran Kulanthaivel
- Department of Biomedical Science, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Kamalendra Singh
- Bond Life Sciences Center, Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, USA
| | - Narcisse Joseph
- Department of Medical Microbiology, Universiti Putra Malaysia, Kuala Lumpur, Malaysia
| | - Vijayakumar Velu
- Division of Microbiology and Immunology, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Emory National Primate Research Center, Emory Vaccine Center, Atlanta, Georgia, USA
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Esaki M Shankar
- Infection and Inflammation, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| | - Sivadoss Raju
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu, India
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20
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Lebatteux D, Soudeyns H, Boucoiran I, Gantt S, Diallo AB. Machine learning-based approach KEVOLVE efficiently identifies SARS-CoV-2 variant-specific genomic signatures. PLoS One 2024; 19:e0296627. [PMID: 38241279 PMCID: PMC10798494 DOI: 10.1371/journal.pone.0296627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 12/07/2023] [Indexed: 01/21/2024] Open
Abstract
Machine learning was shown to be effective at identifying distinctive genomic signatures among viral sequences. These signatures are defined as pervasive motifs in the viral genome that allow discrimination between species or variants. In the context of SARS-CoV-2, the identification of these signatures can assist in taxonomic and phylogenetic studies, improve in the recognition and definition of emerging variants, and aid in the characterization of functional properties of polymorphic gene products. In this paper, we assess KEVOLVE, an approach based on a genetic algorithm with a machine-learning kernel, to identify multiple genomic signatures based on minimal sets of k-mers. In a comparative study, in which we analyzed large SARS-CoV-2 genome dataset, KEVOLVE was more effective at identifying variant-discriminative signatures than several gold-standard statistical tools. Subsequently, these signatures were characterized using a new extension of KEVOLVE (KANALYZER) to highlight variations of the discriminative signatures among different classes of variants, their genomic location, and the mutations involved. The majority of identified signatures were associated with known mutations among the different variants, in terms of functional and pathological impact based on available literature. Here we showed that KEVOLVE is a robust machine learning approach to identify discriminative signatures among SARS-CoV-2 variants, which are frequently also biologically relevant, while bypassing multiple sequence alignments. The source code of the method and additional resources are available at: https://github.com/bioinfoUQAM/KEVOLVE.
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Affiliation(s)
- Dylan Lebatteux
- Department of Computer Science, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Hugo Soudeyns
- CHU Sainte-Justine Research Centre, Montréal, Québec, Canada
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
- Department of Pediatrics, Faculty of Medicine, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Isabelle Boucoiran
- Department of Obstetrics and Gynecology, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Soren Gantt
- CHU Sainte-Justine Research Centre, Montréal, Québec, Canada
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
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21
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Mandal M, Mandal S. Spatiotemporal genome diversity of SARS-CoV-2 in wastewater: a two-year global epidemiological study. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 196:44. [PMID: 38102322 DOI: 10.1007/s10661-023-12228-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023]
Abstract
Wastewater surveillance locally and globally is important for the investigation of the molecular epidemiological features of SARS-CoV-2 in the environment. The current study investigated the genomic diversity and mutation profile of SARS-CoV-2 variants in wastewater for the period spanning COVID-19 pandemic up to December, 2022. A total of 3618 complete SARS-CoV-2 genome sequences from waste water samples submitted to the GISAID database were retrieved. The SARS-CoV-2 sequences were subjected to pairwise alignment against reference, followed by clade and lineage assignment (based on Nextstrain, GISAID and Pango), distance metric phylogenetic analysis, and detection of substitution mutations. Following GISAID, Nextstrain, and Pango nomenclatures, an overall agreement in clade and lineage determination in wastewater samples was observed. There was successive appearance, dissemination, and disappearance of SARS-CoV-2 lineages along time in wastewater. The SARS-CoV-2 genomes from wastewater were clustered into the variants of concern (VOC) as Alpha GRY (B.1.1.7 + Q.7), Delta GK (B.1.617.2 + AY.*), and Omicron GRA (BA.1*, BA.2* + B.1.1.529, BA.5*). The evolutionary rate was 9.63e-04 substitutions/site/year for SARS-CoV-2 in wastewater. B.1.1.7 was less prevalent than B.1.617.2 in 2021, appeared in succession, and BA.1, BA.2, BA.5 were serially detected in 2022, the latter strain continued to persist in wastewater. The N501Y, E484K/Q, K417N/T, L452R, T478K spike substitutions remained dominant attribute of SARS-CoV-2 VOCs. The study underlines the importance of wastewater surveillance for enumerating spatiotemporal diversity of SARS-CoV-2 variants and mutations, which might pave the way for novel antiviral and vaccine designing towards management and prevention of SARS-CoV-2 infection.
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Affiliation(s)
- Manisha Mandal
- Department of Physiology, MGM Medical College, Kishanganj, 855107, India
| | - Shyamapada Mandal
- Department of Zoology, University of Gour Banga, Malda, 732103, West Bengal, India.
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22
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Noh E, Hong J, Yoo J, Jung J. Inference and forecasting phase shift regime of COVID-19 sub-lineages with a Markov-switching model. Microbiol Spectr 2023; 11:e0166923. [PMID: 37811981 PMCID: PMC10714866 DOI: 10.1128/spectrum.01669-23] [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: 04/20/2023] [Accepted: 08/23/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE Using regime-switching models, we attempted to determine whether there is a link between changes in severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) variants and infection waves, as well as forecasting new SARS-Cov-2 variants. We believe that our study makes a significant contribution to the field because it proposes a new approach for forecasting the ongoing pandemic, and the spread of other infectious diseases, using a statistical model which incorporates unpredictable factors such as human behavior, political factors, and cultural beliefs.
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Affiliation(s)
- Eul Noh
- Freddie Mac, Tysons Corner, Virginia, USA
| | - Jinwook Hong
- Artificial Intelligence and Big-Data Convergence Center, Gil Medical Center, Gachon University College of Medicine, Incheon, South Korea
| | - Joonkyung Yoo
- Department of Economics, Rutgers University--New Brunswick, New Brunswick, New Jersey, USA
| | - Jaehun Jung
- Artificial Intelligence and Big-Data Convergence Center, Gil Medical Center, Gachon University College of Medicine, Incheon, South Korea
- Department of Preventive Medicine, Gachon University College of Medicine, Incheon, South Korea
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23
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Ghosh AK, Shahabi D, Imhoff MEC, Kovela S, Sharma A, Hattori SI, Higashi-Kuwata N, Mitsuya H, Mesecar AD. SARS-CoV-2 papain-like protease (PLpro) inhibitory and antiviral activity of small molecule derivatives for drug leads. Bioorg Med Chem Lett 2023; 96:129489. [PMID: 37770002 PMCID: PMC10842477 DOI: 10.1016/j.bmcl.2023.129489] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
We report here the synthesis and biological evaluation of a series of small molecule SARS-CoV-2 PLpro inhibitors. We compared the activity of selected compounds in both SARS-CoV-1 and SARS-CoV-2 PLpro inhibitory and antiviral assays. We have synthesized and evaluated several new structural variants of previous leads against SARS-CoV-2 PLpro. The replacement of the carboxamide functionality with sulfonamide derivatives resulted in PLpro inhibitors with potent PLpro inhibitory and antiviral activity in VeroE6 cells similar to GRL0617. To obtain molecular insight, we created an optimized model of a potent sulfonamide derivative in the SARS-CoV-2 PLpro active site.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 USA.
| | - Dana Shahabi
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 USA
| | | | - Satish Kovela
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 USA
| | - Ashish Sharma
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 USA
| | - Shin-Ichiro Hattori
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655 Japan
| | - Nobuyo Higashi-Kuwata
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655 Japan
| | - Hiroaki Mitsuya
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655 Japan; Department of Clinical Sciences, Kumamoto University Hospital, Kumamoto 860-8556 Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch National Cancer Institute, Bethesda, MD 20892 USA
| | - Andrew D Mesecar
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 USA
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24
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Springer DN, Reuberger E, Borsodi C, Puchhammer-Stöckl E, Weseslindtner L. Comparison of anti-nucleocapsid antibody assays for the detection of SARS-CoV-2 Omicron vaccine breakthroughs after various intervals since the infection. J Med Virol 2023; 95:e29229. [PMID: 37966995 DOI: 10.1002/jmv.29229] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/06/2023] [Accepted: 11/02/2023] [Indexed: 11/17/2023]
Abstract
Antibody assays with the nucleocapsid (NC) protein as the target antigen can identify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections when polymerase chain reaction (PCR) analyses are unavailable. Regarding the kinetics of NC-specific antibodies, vaccine breakthroughs with Omicron subvariants may differ from infections with the ancestral wild-type virus. Therefore, we evaluated which assays have the highest sensitivity for detecting NC-specific antibodies after various intervals since breakthrough infections with an Omicron subvariant. The study included 279 samples from vaccinated subjects who experienced PCR-confirmed Omicron breakthrough infections between 21 and 266 days before sampling. The samples were comparatively assessed with the Elecsys® Anti-SARS-CoV-2 N (Roche), the Anti-SARS-CoV-2-NCP-ELISA (Euroimmun), the recomLine SARS-CoV-2 IgG (Mikrogen), and the SARS-CoV-2 ViraChip IgG assays (Viramed). In the whole cohort, the Elecsys® Anti-SARS-CoV-2 N assay displayed the highest sensitivity (93%, p < 0.0001), followed by the recomLine SARS-CoV-2 IgG assay (70%), the SARS-CoV-2 ViraChip IgG assay (41%) and the Anti-SARS-CoV-2-NCP-ELISA (35%). Although measured antibody levels and time-dependent sensitivities differed, the extent of the antibody decrease was similar among all assays. As demonstrated by this study, manufacturer-dependent differences in the sensitivities of NC-specific antibody assays should be considered when serology is applied to link previous SARS-CoV-2 infections with potential post-COVID sequelae.
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25
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Ellis LP, Hess O, Huynh KLA, Bearman G, Kang L, Doern CD. A comparison of severity of illness between the SARS-CoV-2 Omicron variant and Delta variant. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2023; 3:e188. [PMID: 38028915 PMCID: PMC10654945 DOI: 10.1017/ash.2023.453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 12/01/2023]
Abstract
Background The COVID-19 pandemic has disproportionally affected traditionally marginalized groups. Both the Delta and Omicron variants raised concern amongst public health officials due to potentially higher infectivity rates and disease severity than prior variants. This study sought to compare disease severity between adults infected with the Omicron variant and adults infected with the Delta variant who presented to the Emergency Department at an academic, safety-net hospital in Virginia. Methods This retrospective cohort study used electronic medical record data of patients who presented to the Emergency Department and received a positive SARS-CoV-2 test between September 1, 2021, and January 31, 2022. Positive tests were stratified by genotypic variant through whole genome sequencing. Participants with the Omicron variant were propensity scores matched with individuals with the Delta variant. Results Among 500 Delta and 500 Omicron participants, 279 propensity score-matched pairs were identified. Participants were predominantly unvaccinated, with medical comorbidities, and self-identified as Black. Individuals infected with the Delta variant had more severe disease compared to those with the Omicron variant, regardless of vaccination status. Patients with kidney, liver, and respiratory disease, as well as cancer, are at higher risk for severe disease. Patients with 2 doses of COVID-19 immunization trended toward less severe disease. Conclusions Overall, these data further support the literature regarding the disproportionate effects of the COVID-19 pandemic on vulnerable patient populations - such as those with limited access to care, people of color, and those with chronic medical conditions - and can be used to inform public health interventions.
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Affiliation(s)
- Laura Peyton Ellis
- Obstetrics and Gynecology Residency Program, University of Connecticut, Farmington, CT, USA
| | - Olivia Hess
- School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Khoa Le Anh Huynh
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Gonzalo Bearman
- Richard P. Wenzel Professor of Medicine, Chair, Division of Infectious Diseases, Virginia Commonwealth University, Richmond, VA, USA
- Antimicrobial Stewardship and Healthcare Epidemiology, Cambridge University Press, Cambridge, UK
| | - Le Kang
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Christopher D. Doern
- Microbiology & Pathology and Pediatrics, Virginia Commonwealth University, Richmond, VA, USA
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26
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Lo Presti A, Di Martino A, Ambrosio L, De Sabato L, Knijn A, Vaccari G, Di Bartolo I, Morabito S, Terregino C, Fusaro A, Monne I, Giussani E, Tramuto F, Maida CM, Mazzucco W, Costantino C, Rueca M, Giombini E, Gruber CEM, Capobianchi MR, Palamara AT, Stefanelli P, on behalf of the Italian Genomic Laboratory Network. Tracking the Selective Pressure Profile and Gene Flow of SARS-CoV-2 Delta Variant in Italy from April to October 2021 and Frequencies of Key Mutations from Three Representative Italian Regions. Microorganisms 2023; 11:2644. [PMID: 38004656 PMCID: PMC10673055 DOI: 10.3390/microorganisms11112644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
The SARS-CoV-2 Delta variant of concern (VOC) was often associated with serious clinical course of the COVID-19 disease. Herein, we investigated the selective pressure, gene flow and evaluation on the frequencies of mutations causing amino acid substitutions in the Delta variant in three Italian regions. A total of 1500 SARS-CoV-2 Delta genomes, collected in Italy from April to October 2021 were investigated, including a subset of 596 from three Italian regions. The selective pressure and the frequency of amino acid substitutions and the prediction of their possible impact on the stability of the proteins were investigated. Delta variant dataset, in this study, identified 68 sites under positive selection: 16 in the spike (23.5%), 11 in nsp2 (16.2%) and 10 in nsp12 (14.7%) genes. Three of the positive sites in the spike were located in the receptor-binding domain (RBD). In Delta genomes from the three regions, 6 changes were identified as very common (>83.7%), 4 as common (>64.0%), 21 at low frequency (2.1%-25.0%) and 29 rare (≤2.0%). The detection of positive selection on key mutations may represent a model to identify recurrent signature mutations of the virus.
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Affiliation(s)
- Alessandra Lo Presti
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Angela Di Martino
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Luigina Ambrosio
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Luca De Sabato
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Arnold Knijn
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Gabriele Vaccari
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Ilaria Di Bartolo
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Stefano Morabito
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Calogero Terregino
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Alice Fusaro
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Isabella Monne
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Edoardo Giussani
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Fabio Tramuto
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Carmelo Massimo Maida
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Walter Mazzucco
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Claudio Costantino
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Martina Rueca
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
| | - Emanuela Giombini
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
| | - Cesare Ernesto Maria Gruber
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
| | - Maria Rosaria Capobianchi
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
- Saint Camillus International University of Health Sciences, Via di Sant’Alessandro, 8, 00131 Rome, Italy
- Department of Infectious Tropical Diseases and Microbiology, Sacro Cuore Don Calabria Hospital I.R.C.C.S., Via Don A. Sempreboni 5, 37024 Negrar di Valpolicella, Italy
| | - Anna Teresa Palamara
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Paola Stefanelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
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27
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Basak S, Kayet P, Ghosh M, Chatterjee J, Dutta S. Emergence of Genomic Diversity in the Spike Protein of the "Omicron" Variant. Viruses 2023; 15:2132. [PMID: 37896909 PMCID: PMC10612054 DOI: 10.3390/v15102132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus) has constantly been evolving into different forms throughout its spread in the population. Emerging SARS-CoV-2 variants, predominantly the variants of concern (VOCs), could have an impact on the virus spread, pathogenicity, and diagnosis. The recently emerged "Omicron" variant has exhibited rapid transmission and divergence. The spike protein of SARS-CoV-2 has consistently been appearing as the mutational hotspot of all these VOCs. In order to determine a deeper understanding of the recently emerged and extremely divergent "Omicron", a study of amino acid usage patterns and their substitution patterns was performed and compared with those of the other four successful variants of concern ("Alpha", "Beta", "Gamma", and "Delta"). We observed that the amino acid usage of "Omicron" has a distinct pattern that distinguishes it from other VOCs and is significantly correlated with the increased hydrophobicity in spike proteins. We observed an increase in the non-synonymous substitution rate compared with the other four VOCs. Considering the phylogenetic relationship, we hypothesized about the functional interdependence between recombination and the mutation rate that might have resulted in a shift in the optimum of the mutation rate for the evolution of the "Omicron" variant. The results suggest that for improved disease prevention and control, more attention should be given to the significant genetic differentiation and diversity of newly emerging variants.
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Affiliation(s)
- Surajit Basak
- Division of Bioinformatics, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Pratanu Kayet
- Division of Bioinformatics, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Manisha Ghosh
- Division of Bioinformatics, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Joyeeta Chatterjee
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry 605014, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
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Padhi AK, Kalita P, Maurya S, Poluri KM, Tripathi T. From De Novo Design to Redesign: Harnessing Computational Protein Design for Understanding SARS-CoV-2 Molecular Mechanisms and Developing Therapeutics. J Phys Chem B 2023; 127:8717-8735. [PMID: 37815479 DOI: 10.1021/acs.jpcb.3c04542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
The continuous emergence of novel SARS-CoV-2 variants and subvariants serves as compelling evidence that COVID-19 is an ongoing concern. The swift, well-coordinated response to the pandemic highlights how technological advancements can accelerate the detection, monitoring, and treatment of the disease. Robust surveillance systems have been established to understand the clinical characteristics of new variants, although the unpredictable nature of these variants presents significant challenges. Some variants have shown resistance to current treatments, but innovative technologies like computational protein design (CPD) offer promising solutions and versatile therapeutics against SARS-CoV-2. Advances in computing power, coupled with open-source platforms like AlphaFold and RFdiffusion (employing deep neural network and diffusion generative models), among many others, have accelerated the design of protein therapeutics with precise structures and intended functions. CPD has played a pivotal role in developing peptide inhibitors, mini proteins, protein mimics, decoy receptors, nanobodies, monoclonal antibodies, identifying drug-resistance mutations, and even redesigning native SARS-CoV-2 proteins. Pending regulatory approval, these designed therapies hold the potential for a lasting impact on human health and sustainability. As SARS-CoV-2 continues to evolve, use of such technologies enables the ongoing development of alternative strategies, thus equipping us for the "New Normal".
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Affiliation(s)
- Aditya K Padhi
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India
| | - Parismita Kalita
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Shweata Maurya
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
- Department of Zoology, School of Life Sciences, North-Eastern Hill University, Shillong 793022, India
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Maldonado-Cabrera A, Colin-Vilchis JA, Haque U, Velazquez C, Alvarez Villaseñor AS, Magdaleno-Márquez LE, Calleros-Muñoz CI, Figueroa-Enríquez KF, Angulo-Molina A, Gallego-Hernández AL. SARS-CoV-2 Variants of Concern and Clinical Severity in the Mexican Pediatric Population. Infect Dis Rep 2023; 15:535-548. [PMID: 37737000 PMCID: PMC10514801 DOI: 10.3390/idr15050053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/23/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants of concern (VOCs) presents global heterogeneity, and their relative effect on pediatric severity is still limited. In this study, we associate VOCs with pediatric clinical severity outcomes in Mexico. Bioinformatics methods were used to characterize VOCs and single amino acid (aa) mutations in 75,348 SARS-CoV-2 genetic sequences from February 2020 to October 2022. High-predominance VOCs groups were calculated and subsequently associated with 372,989 COVID-19 clinical pediatric outcomes. We identified 21 high-frequency mutations related to Omicron lineages with an increased prevalence in pediatric sequences compared to adults. Alpha and the other lineages had a significant increase in case fatality rate (CFR), intensive critical unit (ICU) admission, and automated mechanical ventilation (AMV). Furthermore, a logistic model with age-adjusted variables estimated an increased risk of hospitalization, ICU/AMV, and death in Gamma and Alpha, in contrast to the other lineages. We found that, regardless of the VOCs lineage, infant patients presented the worst severity prognoses. Our findings improve the understanding of the impact of VOCs on pediatric patients across time, regions, and clinical outcomes. Enhanced understanding of the pediatric severity for VOCs would enable the development and improvement of public health strategies worldwide.
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Affiliation(s)
- Anahí Maldonado-Cabrera
- Department of Chemical Biological Sciences, University of Sonora, Hermosillo 83000, Mexico; (A.M.-C.); (C.V.)
- Department of Epidemiology, Family Medicine Unit No. 37, Mexican Social Security Institute (IMSS), Hermosillo 83260, Mexico
| | | | - Ubydul Haque
- Rutgers Global Health Institute, New Brunswick, NJ 08901, USA;
- Department of Biostatistics and Epidemiology, School of Public Health, Rutgers University, Piscataway, NJ 08854, USA
| | - Carlos Velazquez
- Department of Chemical Biological Sciences, University of Sonora, Hermosillo 83000, Mexico; (A.M.-C.); (C.V.)
| | | | | | | | | | - Aracely Angulo-Molina
- Department of Chemical Biological Sciences, University of Sonora, Hermosillo 83000, Mexico; (A.M.-C.); (C.V.)
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, 4132 Muttenz, Switzerland
| | - Ana Lucía Gallego-Hernández
- Department of Chemical Biological Sciences, University of Sonora, Hermosillo 83000, Mexico; (A.M.-C.); (C.V.)
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Kandeel A, Moatasim Y, Fahim M, Bahaaeldin H, El-Shesheny R, Roshdy WH, Kamel MN, Shawky S, Gomaa M, Naguib A, Guindy NE, Deghedy O, Kamel R, Khalifa M, Galal R, Hassany M, Mahmoud G, Kandeil A, Afifi S, Mohsen A, Fattah MA, Kayali G, Ali MA, Abdelghaffar K. Comparison of SARS-Cov-2 omicron variant with the previously identified SARS-Cov-2 variants in Egypt, 2020-2022: insight into SARS-Cov-2 genome evolution and its impact on epidemiology, clinical picture, disease severity, and mortality. BMC Infect Dis 2023; 23:542. [PMID: 37596534 PMCID: PMC10439637 DOI: 10.1186/s12879-023-08527-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 08/10/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND The o severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic has killed millions of people and caused widespread concern around the world. Multiple genetic variants of SARS-CoV-2 have been identified as the pandemic continues. Concerns have been raised about high transmissibility and lower vaccine efficacy against omicron. There is an urgent need to better describe how omicron will impact clinical presentation and vaccine efficacy. This study aims at comparing the epidemiologic, clinical, and genomic characteristics of the omicron variant prevalent during the fifth wave with those of other VOCs between May 2020 and April 2022. METHODS Epidemiological data were obtained from the National Electronic Diseases Surveillance System. Secondary data analysis was performed on all confirmed COVID-19 patients. Descriptive data analysis was performed for demographics and patient outcome and the incidence of COVID-19 was calculated as the proportion of SARS-CoV-2 confirmed patients out of the total population of Egypt. Incidence and characteristics of the omicron cohort from January- April 2022, were compared to those confirmed from May 2020-December 2021. We performed the whole-genome sequencing of SARS-CoV-2 on 1590 specimens using Illumina sequencing to describe the circulation of the virus lineages in Egypt. RESULTS A total of 502,629 patients enrolled, including 60,665 (12.1%) reported in the fifth wave. The incidence rate of omicron was significantly lower than the mean of incidences in the previous subperiod (60.1 vs. 86.3/100,000 population, p < 0.001). Symptoms were reported less often in the omicron cohort than in patients with other variants, with omicron having a lower hospitalization rate and overall case fatality rate as well. The omicron cohort tended to stay fewer days at the hospital than did those with other variants. We analyzed sequences of 2433 (1590 in this study and 843 were obtained from GISAID platform) Egyptian SARS-CoV-2 full genomes. The first wave that occurred before the emergence of global variants of concern belonged to the B.1 clade. The second and third waves were associated with C.36. Waves 4 and 5 included B.1.617.2 and BA.1 clades, respectively. CONCLUSIONS The study indicated that Omicron-infected patients had milder symptoms and were less likely to be hospitalized; however, patients hospitalized with omicron had a more severe course and higher fatality rates than those hospitalized with other variants. Our findings demonstrate the importance of combining epidemiological data and genomic analysis to generate actionable information for public health decision-making.
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Affiliation(s)
- Amr Kandeel
- Preventive Sector, Ministry of Health and Population, Cairo, Egypt
| | - Yassmin Moatasim
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Manal Fahim
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, Cairo, Egypt
| | - Hala Bahaaeldin
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, Cairo, Egypt.
| | - Rabeh El-Shesheny
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Wael H Roshdy
- Central Public Health Laboratory, Ministry of Health and Population, Cairo, Egypt
| | - Mina N Kamel
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Shaymaa Shawky
- Central Public Health Laboratory, Ministry of Health and Population, Cairo, Egypt
| | - Mokhtar Gomaa
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Amel Naguib
- Central Public Health Laboratory, Ministry of Health and Population, Cairo, Egypt
| | - Nancy El Guindy
- Central Public Health Laboratory, Ministry of Health and Population, Cairo, Egypt
| | - Ola Deghedy
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, Cairo, Egypt
| | - Reham Kamel
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, Cairo, Egypt
| | - Mohamed Khalifa
- Central Public Health Laboratory, Ministry of Health and Population, Cairo, Egypt
| | - Ramy Galal
- Public Health Initiatives, Cairo, 11613, Egypt
| | - Mohamed Hassany
- National Hepatology and Tropical Medicine Research Institute, Ministry of Health and Population, Cairo, 11613, Egypt
| | - Galal Mahmoud
- Central Public Health Laboratory, Ministry of Health and Population, Cairo, Egypt
| | - Ahmed Kandeil
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Salma Afifi
- Ministry of Health and Population Consultant, Cairo, Egypt
| | - Amira Mohsen
- Community Medicine Department, National Research Centre, Cairo, Egypt
| | - Mohammad Abdel Fattah
- Preventive Sector, Central Administration for Preventive Affairs, Ministry of Health and Population, Cairo, Egypt
| | | | - Mohamed A Ali
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza, 12622, Egypt
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Askarian M, Movahedi M, Vardanjani HM, Askarian A, Ghotbabadi ZR. Roadmap to recovery: Implemented and attitude toward school reopening strategies during the COVID-19 pandemic, a scoping review. JOURNAL OF EDUCATION AND HEALTH PROMOTION 2023; 12:235. [PMID: 37727417 PMCID: PMC10506747 DOI: 10.4103/jehp.jehp_1160_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/16/2022] [Indexed: 09/21/2023]
Abstract
The novel coronavirus disease 2019 (COVID-19) has had various financial and life impacts on the world's population. Schools' regular activity and function during the pandemic require balancing the repercussions of suspending in-person education versus health threats. Furthermore, children are one of the prominent victims of the restricted quarantine strategies' effects, which may make them vulnerable to various mental health problems. In this study, we reviewed previously reported strategies and roadmaps regarding the reopening of schools during the COVID-19 pandemic. The following databases were searched from October to December 2021, via multi-step search strategies for "COVID-19," "coronavirus," "school reopening," "roadmaps," "reopening," and "reopening strategies": Google Scholar, PubMed, Scopus, and Web of Science. A total of five papers with roadmaps focusing on reopening schools were included in this study. Fundamental issues and principles of these reviewed roadmaps were: 1) protecting the high-risk students and staff physically and mentally, 2) accelerating the vaccination of essential workers, staff, parents, and students, and 3) improving the COVID-19 testing capacity. Roadmaps for the reopening of the schools should describe some phases and steps for their strategies. Current roadmaps have not mentioned any phases and timelines for this process. Describing some health metrics in the roadmaps for progressing to the next step or returning to the previous ones is also necessary for all roadmaps and should be considered in further studies.
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Affiliation(s)
- Mehrdad Askarian
- Department of Community Medicine, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran, Health Behavior Science Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Movahedi
- Institute of Health Policy, Management, and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Hossein M. Vardanjani
- MPH Department, School of Medicine, Research Center for Traditional Medicine and History of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ardalan Askarian
- Student, College of Arts and Science, University of Saskatchewan, Saskatoon, Canada
| | - Zahra R. Ghotbabadi
- MPH Department, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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Xing Y, Li Y, Feng L, Huo R, Ma X, Dong Y, Liu D, Niu Y, Tian X, Chen E. Predictors of COVID-19 Severity in Elderly Patients Infected by Omicron in China, 18 December 2022-5 February 2023. Infect Drug Resist 2023; 16:4505-4518. [PMID: 37457796 PMCID: PMC10349581 DOI: 10.2147/idr.s418622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023] Open
Abstract
Purpose To analyze the clinical characteristics and prognosis of patients hospitalized with non-severe, severe pneumonia and death in Omicron COVID-19. Patients and Methods We collected clinical data from 118 patients with COVID-19 in China from 18 December, 2022 and 5 February, 2023. According to the outcome, the patients were divided into non-severe group, severe group and death group. Subsequently, we statistically analyzed the general condition, clinical manifestations, laboratory parameters, NLR, MLR, PLR and HALP of these groups. We also retrospectively analyzed the possible factors affecting the prognostic regression of patients with COVID-19. Results A total of 118 COVID-19 patients were enrolled in this study, including 64 non-severe patients, 38 severe patients and 16 death patients. Compared with the non-severe group, T lymphocytes, B lymphocytes, Th1, Th2, Th17, Treg cells, IgA, IgG, IgM in the severe and death groups decreased more significantly (P<0.05). The levels of myocardial markers, ALT, AST, BUN, Cr, D-dimer, fibrinogen, NLR, MLR and PLR in the severe and death groups were significantly higher than those in the non-severe group (P<0.05). The level of HALP was significantly lower than that of non-severe group (P<0.05). MLR is not only an independent risk factor for the transition from non-severe to severe disease, but also an independent risk factor for predicting the possibility of death in COVID-19 patients. Conclusion The analysis of COVID-19 patients in China showed that severe patients were older, more likely to have related complications, lower lymphocyte count, liver and kidney function disorder, glucose and lipid metabolism disorders, myocardial injury, and abnormal coagulation function, suggesting the need for early anticoagulant therapy. In addition, NLR, MLR, PLR and HALP can be used as biomarkers to evaluate the severity and prognosis of COVID-19 patients.
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Affiliation(s)
- Yanqing Xing
- The Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Yupeng Li
- The Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Liting Feng
- The Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Rujie Huo
- The Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Xinkai Ma
- The Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Yanting Dong
- The Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Dai Liu
- The Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Yuheng Niu
- The First Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Xinrui Tian
- The Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Erjing Chen
- The Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
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Pinho CT, Vidal AF, Negri Rocha TC, Oliveira RRM, da Costa Barros MC, Closset L, Azevedo-Pinheiro J, Braga-da-Silva C, Silva CS, Magalhães LL, do Carmo Pinto PD, Souza GBS, dos Santos Vieira JR, Burbano RMR, de Sousa MS, de Souza JES, Nunes G, da Silva MB, da Costa PF, Salgado CG, Sousa RCM, Degrave WMS, Ribeiro-dos-Santos Â, Oliveira G. Transmission dynamics of SARS-CoV-2 variants in the Brazilian state of Pará. Front Public Health 2023; 11:1186463. [PMID: 37790714 PMCID: PMC10543262 DOI: 10.3389/fpubh.2023.1186463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/30/2023] [Indexed: 10/05/2023] Open
Abstract
Introduction After three years since the beginning of the pandemic, the new coronavirus continues to raise several questions regarding its infectious process and host response. Several mutations occurred in different regions of the SARS-CoV-2 genome, such as in the spike gene, causing the emergence of variants of concern and interest (VOCs and VOIs), of which some present higher transmissibility and virulence, especially among patients with previous comorbidities. It is essential to understand its spread dynamics to prevent and control new biological threats that may occur in the future. In this population_based retrospective observational study, we generated data and used public databases to understand SARS-CoV-2 dynamics. Methods We sequenced 1,003 SARS-CoV-2 genomes from naso-oropharyngeal swabs and saliva samples from Pará from May 2020 to October 2022. To gather epidemiological data from Brazil and the world, we used FIOCRUZ and GISAID databases. Results Regarding our samples, 496 (49.45%) were derived from female participants and 507 (50.55%) from male participants, and the average age was 43 years old. The Gamma variant presented the highest number of cases, with 290 (28.91%) cases, followed by delta with 53 (5.28%). Moreover, we found seven (0.69%) Omicron cases and 651 (64.9%) non-VOC cases. A significant association was observed between sex and the clinical condition (female, p = 8.65e-08; male, p = 0.008961) and age (p = 3.6e-10). Discussion Although gamma had been officially identified only in December 2020/January 2021, we identified a gamma case from Belém (capital of Pará State) dated May 2020 and three other cases in October 2020. This indicates that this variant was circulating in the North region of Brazil several months before its formal identification and that Gamma demonstrated its actual transmission capacity only at the end of 2020. Furthermore, the public data analysis showed that SARS-CoV-2 dispersion dynamics differed in Brazil as Gamma played an important role here, while most other countries reported a new infection caused by the Delta variant. The genetic and epidemiological information of this study reinforces the relevance of having a robust genomic surveillance service that allows better management of the pandemic and that provides efficient solutions to possible new disease-causing agents.
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Affiliation(s)
- Catarina T. Pinho
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | | | | | | | - Maria Clara da Costa Barros
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Laura Closset
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Jhully Azevedo-Pinheiro
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Cíntia Braga-da-Silva
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Caio Santos Silva
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Leandro L. Magalhães
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Pablo Diego do Carmo Pinto
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Giordano Bruno Soares Souza
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - José Ricardo dos Santos Vieira
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | | | | | - Jorge Estefano Santana de Souza
- Programa de Pós-Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
- Bioinformatics Núcleo Multidisciplinar de Bioinformática, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | | | - Moises Batista da Silva
- Laboratório de Dermatologia e Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, Pará, Brazil
| | - Patrícia Fagundes da Costa
- Laboratório de Dermatologia e Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, Pará, Brazil
| | - Claudio Guedes Salgado
- Laboratório de Dermatologia e Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, Pará, Brazil
| | | | - Wim Maurits Sylvain Degrave
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ândrea Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
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Gomez-Gonzalez E, Muñoz O, Gomez-Martin JC, Aceituno-Castro J, Fernandez-Muñoz B, Navas-Garcia JM, Barriga-Rivera A, Fernandez-Lizaranzu I, Munoz-Gonzalez FJ, Parrilla-Giraldez R, Requena-Lancharro D, Gil-Gamboa P, Ramos JL, Rosell-Valle C, Gomez-Gonzalez C, Martin-Lopez M, Relimpio-Lopez MI, Perales-Esteve MA, Puppo-Moreno A, Garcia-Cozar FJ, Olvera-Collantes L, de Los Santos-Trigo S, Gomez E, Sanchez-Pernaute R, Padillo-Ruiz J, Marquez-Rivas J. Polarimetric imaging for the detection of synthetic models of SARS-CoV-2: A proof of concept. JOURNAL OF QUANTITATIVE SPECTROSCOPY & RADIATIVE TRANSFER 2023; 302:108567. [PMID: 36945203 PMCID: PMC9987604 DOI: 10.1016/j.jqsrt.2023.108567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 03/04/2023] [Accepted: 03/04/2023] [Indexed: 06/18/2023]
Abstract
Objective To conduct a proof-of-concept study of the detection of two synthetic models of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using polarimetric imaging. Approach Two SARS-CoV-2 models were prepared as engineered lentiviruses pseudotyped with the G protein of the vesicular stomatitis virus, and with the characteristic Spike protein of SARS-CoV-2. Samples were prepared in two biofluids (saline solution and artificial saliva), in four concentrations, and deposited as 5-µL droplets on a supporting plate. The angles of maximal degree of linear polarization (DLP) of light diffusely scattered from dry residues were determined using Mueller polarimetry from87 samples at 405 nm and 514 nm. A polarimetric camera was used for imaging several samples under 380-420 nm illumination at angles similar to those of maximal DLP. Per-pixel image analysis included quantification and combination of polarization feature descriptors in 475 samples. Main results The angles (from sample surface) of maximal DLP were 3° for 405 nm and 6° for 514 nm. Similar viral particles that differed only in the characteristic spike protein of the SARS-CoV-2, their corresponding negative controls, fluids, and the sample holder were discerned at 10-degree and 15-degree configurations. Significance Polarimetric imaging in the visible spectrum may help improve fast, non-contact detection and identification of viral particles, and/or other microbes such as tuberculosis, in multiple dry fluid samples simultaneously, particularly when combined with other imaging modalities. Further analysis including realistic concentrations of real SARS-CoV-2 viral particles in relevant human fluids is required. Polarimetric imaging under visible light may contribute to a fast, cost-effective screening of SARS-CoV-2 and other pathogens when combined with other imaging modalities.
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Affiliation(s)
- Emilio Gomez-Gonzalez
- Group of Interdisciplinary Physics, Department of Applied Physics III at the ETSI Engineering School, Universidad de Sevilla, Seville 41092, Spain
- Institute of Biomedicine of Seville, Spain
| | - Olga Muñoz
- Cosmic Dust Laboratory, Instituto de Astrofísica de Andalucía, CSIC, Granada 18008, Spain
| | | | - Jesus Aceituno-Castro
- Cosmic Dust Laboratory, Instituto de Astrofísica de Andalucía, CSIC, Granada 18008, Spain
- Centro Astronomico Hispano Alemán, Almeria 04550, Spain
| | - Beatriz Fernandez-Muñoz
- Unidad de Producción y Reprogramación Celular, Red Andaluza de Diseño y Traslación de Terapias Avanzadas, Fundacion Publica Andaluza Progreso y Salud, Sevilla 41092, Spain
| | | | - Alejandro Barriga-Rivera
- Group of Interdisciplinary Physics, Department of Applied Physics III at the ETSI Engineering School, Universidad de Sevilla, Seville 41092, Spain
- School of Biomedical Engineering, The University of Sydney, NSW 2006, Australia
| | - Isabel Fernandez-Lizaranzu
- Group of Interdisciplinary Physics, Department of Applied Physics III at the ETSI Engineering School, Universidad de Sevilla, Seville 41092, Spain
- Institute of Biomedicine of Seville, Spain
| | - Francisco Javier Munoz-Gonzalez
- Group of Interdisciplinary Physics, Department of Applied Physics III at the ETSI Engineering School, Universidad de Sevilla, Seville 41092, Spain
| | | | - Desiree Requena-Lancharro
- Group of Interdisciplinary Physics, Department of Applied Physics III at the ETSI Engineering School, Universidad de Sevilla, Seville 41092, Spain
| | - Pedro Gil-Gamboa
- Group of Interdisciplinary Physics, Department of Applied Physics III at the ETSI Engineering School, Universidad de Sevilla, Seville 41092, Spain
| | - José Luis Ramos
- Cosmic Dust Laboratory, Instituto de Astrofísica de Andalucía, CSIC, Granada 18008, Spain
| | - Cristina Rosell-Valle
- Unidad de Producción y Reprogramación Celular, Red Andaluza de Diseño y Traslación de Terapias Avanzadas, Fundacion Publica Andaluza Progreso y Salud, Sevilla 41092, Spain
| | - Carmen Gomez-Gonzalez
- Service of Intensive Care, University Hospital 'Virgen del Rocio', Sevilla 41013, Spain
| | - Maria Martin-Lopez
- Unidad de Producción y Reprogramación Celular, Red Andaluza de Diseño y Traslación de Terapias Avanzadas, Fundacion Publica Andaluza Progreso y Salud, Sevilla 41092, Spain
| | - Maria Isabel Relimpio-Lopez
- Department of General Surgery, College of Medicine, Universidad de Sevilla, Seville 41009, Spain
- Department of Ophthalmology, University Hospital 'Virgen Macarena', Sevilla 41009, Spain
- OftaRed, Institute of Health 'Carlos III', Madrid 28029, Spain
| | - Manuel A Perales-Esteve
- Group of Interdisciplinary Physics, Department of Applied Physics III at the ETSI Engineering School, Universidad de Sevilla, Seville 41092, Spain
- Department of Electronic Engineering at the ETSI Engineering School, Universidad de Sevilla, Seville 41092, Spain
| | - Antonio Puppo-Moreno
- Institute of Biomedicine of Seville, Spain
- Service of Intensive Care, University Hospital 'Virgen del Rocio', Sevilla 41013, Spain
| | - Francisco Jose Garcia-Cozar
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz, Cadiz 11003, Spain
- Instituto de Investigación e Innovación Biomedica de Cádiz (INIBICA), Cadiz 11009, Spain
| | - Lucia Olvera-Collantes
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz, Cadiz 11003, Spain
- Instituto de Investigación e Innovación Biomedica de Cádiz (INIBICA), Cadiz 11009, Spain
| | | | - Emilia Gomez
- Joint Research Centre, European Commission, Sevilla 41092, Spain
| | - Rosario Sanchez-Pernaute
- Unidad de Producción y Reprogramación Celular, Red Andaluza de Diseño y Traslación de Terapias Avanzadas, Fundacion Publica Andaluza Progreso y Salud, Sevilla 41092, Spain
| | | | - Javier Marquez-Rivas
- Group of Interdisciplinary Physics, Department of Applied Physics III at the ETSI Engineering School, Universidad de Sevilla, Seville 41092, Spain
- Institute of Biomedicine of Seville, Spain
- Service of Neurosurgery, University Hospital 'Virgen del Rocío', Sevilla 41013, Spain
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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: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [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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Radion EI, Mukhin VE, Kholodova AV, Vladimirov IS, Alsaeva DY, Zhdanova AS, Ulasova NY, Bulanova NV, Makarov VV, Keskinov AA, Yudin SM. Functional Characteristics of Serum Anti-SARS-CoV-2 Antibodies against Delta and Omicron Variants after Vaccination with Sputnik V. Viruses 2023; 15:1349. [PMID: 37376648 DOI: 10.3390/v15061349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Anti-SARS-CoV-2 vaccination leads to the production of neutralizing as well as non-neutralizing antibodies. In the current study, we investigated the temporal dynamics of both sides of immunity after vaccination with two doses of Sputnik V against SARS-CoV-2 variants Wuhan-Hu-1 SARS-CoV-2 G614-variant (D614G), B.1.617.2 (Delta), and BA.1 (Omicron). First, we constructed a SARS-CoV-2 pseudovirus assay to assess the neutralization activity of vaccine sera. We show that serum neutralization activity against BA.1 compared to D614G is decreased by 8.16-, 11.05-, and 11.16- fold in 1, 4, and 6 months after vaccination, respectively. Moreover, previous vaccination did not increase serum neutralization activity against BA.1 in recovered patients. Next, we used the ADMP assay to evaluate the Fc-mediated function of vaccine-induced serum antibodies. Our results show that the antibody-dependent phagocytosis triggered by S-proteins of the D614G, B.1.617.2 and BA.1 variants did not differ significantly in vaccinated individuals. Moreover, the ADMP efficacy was retained over up to 6 months in vaccine sera. Our results demonstrate differences in the temporal dynamics of neutralizing and non-neutralizing antibody functions after vaccination with Sputnik V.
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Affiliation(s)
- Elizaveta I Radion
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Schukinskaya 5, Building 1, Moscow 123182, Russia
| | - Vladimir E Mukhin
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Schukinskaya 5, Building 1, Moscow 123182, Russia
| | - Alyona V Kholodova
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Schukinskaya 5, Building 1, Moscow 123182, Russia
| | - Ivan S Vladimirov
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Schukinskaya 5, Building 1, Moscow 123182, Russia
| | - Darya Y Alsaeva
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Schukinskaya 5, Building 1, Moscow 123182, Russia
| | - Anastasia S Zhdanova
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Schukinskaya 5, Building 1, Moscow 123182, Russia
| | - Natalya Y Ulasova
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Schukinskaya 5, Building 1, Moscow 123182, Russia
| | - Natalya V Bulanova
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Schukinskaya 5, Building 1, Moscow 123182, Russia
| | - Valentin V Makarov
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Schukinskaya 5, Building 1, Moscow 123182, Russia
| | - Anton A Keskinov
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Schukinskaya 5, Building 1, Moscow 123182, Russia
| | - Sergey M Yudin
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Schukinskaya 5, Building 1, Moscow 123182, Russia
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Subhadra B, Agrawal R, Pal VK, Chenine AL, Mattathil JG, Singh A. Significant Broad-Spectrum Antiviral Activity of Bi121 against Different Variants of SARS-CoV-2. Viruses 2023; 15:1299. [PMID: 37376598 DOI: 10.3390/v15061299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/12/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has so far infected 762 million people with over 6.9 million deaths worldwide. Broad-spectrum viral inhibitors that block the initial stages of infection by reducing virus binding and proliferation, thereby reducing disease severities, are still an unmet global medical need. We studied Bi121, which is a standardized polyphenolic-rich compound isolated from Pelargonium sidoides, against recombinant vesicular stomatitis virus (rVSV)-pseudotyped SARS-CoV-2S (mutations in the spike protein) of six different variants of SARS-CoV-2. Bi121 was effective at neutralizing all six rVSV-ΔG-SARS-CoV-2S variants. The antiviral activity of Bi121 was also assessed against SARS-CoV-2 variants (USA WA1/2020, Hongkong/VM20001061/2020, B.1.167.2 (Delta), and Omicron) in Vero cells and HEK-ACE2 cell lines using RT-qPCR and plaque assays. Bi121 showed significant antiviral activity against all the four SARS-CoV-2 variants tested, suggesting a broad-spectrum activity. Bi121 fractions generated using HPLC showed antiviral activity in three fractions out of eight against SARS-CoV-2. The dominant compound identified in all three fractions using LC/MS/MS analysis was Neoilludin B. In silico structural modeling studies with Neoilludin B showed that it has a novel RNA-intercalating activity toward RNA viruses. In silico findings and the antiviral activity of this compound against several SARS-CoV-2 variants support further evaluation as a potential treatment of COVID-19.
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Affiliation(s)
- Bobban Subhadra
- Biom Pharmaceutical Corporation, 2203 Industrial Blvd, Sarasota, FL 34234, USA
| | - Ragini Agrawal
- Department of Microbiology and Cell Biology, Center for Infectious Disease Research, Indian Institute of Science (IISc), CV Raman Ave., Bengaluru 560012, India
| | - Virender Kumar Pal
- Department of Microbiology and Cell Biology, Center for Infectious Disease Research, Indian Institute of Science (IISc), CV Raman Ave., Bengaluru 560012, India
| | | | | | - Amit Singh
- Department of Microbiology and Cell Biology, Center for Infectious Disease Research, Indian Institute of Science (IISc), CV Raman Ave., Bengaluru 560012, India
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Wang J, Hu W, Wang K, Yu R, Chang L, Rong Z. Case report: Acute hepatitis in neonates with COVID-19 during the Omicron SARS-CoV-2 variant wave: a report of four cases. Front Pediatr 2023; 11:1179402. [PMID: 37215592 PMCID: PMC10196249 DOI: 10.3389/fped.2023.1179402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 04/11/2023] [Indexed: 05/24/2023] Open
Abstract
Background Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), first emerging in December 2019 and continuously evolving, poses a considerable challenge worldwide. It was reported in the literature that neonates had mild upper respiratory symptoms and a better outcome after Omicron SARS-CoV-2 variant infection, but there was insufficient data about complications and prognosis. Case Presentation In this paper, we present the clinical and laboratory characteristics of four COVID-19 neonate patients with acute hepatitis during the Omicron SARS-CoV-2 variant wave. All patients had a clear history of Omicron exposure and were infected via contact with confirmed caregivers. Low to moderate fever and respiratory symptoms were the primary clinical manifestations, and all patients had a normal liver function at the initial stage of the course. Then, the fever lasted 2 to 4 days, and it was noted that hepatic dysfunction might have occurred 5 to 8 days after the first onset of fever, mainly characterized by moderate ALT and AST elevation (>3 to 10-fold of upper limit). There were no abnormalities in bilirubin levels, blood ammonia, protein synthesis, lipid metabolism, and coagulation. All the patients received hepatoprotective therapy, and transaminase levels gradually decreased to the normal range after 2 to 3 weeks without other complications. Conclusions This is the first case series about moderate to severe hepatitis in COVID-19 neonatal patients via horizontal transmission. Besides fever and respiratory symptoms, the clinical doctor should pay much attention to evaluating the risk of liver function injury after SARS-CoV-2 variants infection, which is usually asymptomatic and has a delayed onset.
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Yuan M, Zhu Y, Liu G, Wang Y, Wang G, Zhang G, Ye L, Qian Z, Liu P. An RBD bispecific antibody effectively neutralizes a SARS-CoV-2 Omicron variant. ONE HEALTH ADVANCES 2023; 1:12. [PMID: 37521533 PMCID: PMC10173222 DOI: 10.1186/s44280-023-00012-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/05/2023] [Accepted: 04/14/2023] [Indexed: 08/01/2023]
Abstract
Potent neutralizing antibodies (nAbs) against SARS-CoV-2 are a promising therapeutic against the ongoing COVID-19 pandemic. However, the continuous emergence of neutralizing antibody escape variants makes it challenging for antibody therapeutics based on monospecific nAbs. Here, we generated an IgG-like bispecific antibody (bsAb), Bi-Nab, based on a pair of human neutralizing antibodies targeting multiple and invariant sites of the spike receptor binding domain (RBD): 35B5 and 32C7. We demonstrated that Bi-Nab exhibited higher binding affinity to the Delta spike protein than its parental antibodies and presented an extended inhibition breadth of preventing RBD binding to angiotensin-converting enzyme 2 (ACE2), the cellular receptor of SARS-CoV-2. In addition, pseudovirus neutralization results showed that Bi-Nab improved the neutralization potency and breadth with a lower half maximum inhibitory concentration (IC50) against wild-type SARS-CoV-2, variants being monitored (VBMs) and variants of concern (VOCs). Notably, the IgG-like Bi-Nab enhanced the neutralizing activity against Omicron variants with potent capabilities for transmission and immune evasion in comparison with its parental monoclonal antibody (mAb) 32C7 and a cocktail (with the lowest IC50 values of 31.6 ng/mL against the Omicron BA.1 and 399.2 ng/mL against the Omicron BA.2), showing evidence of synergistic neutralization potency of Bi-Nab against the Omicron variants. Thus, Bi-Nab represents a feasible and effective strategy against SARS-CoV-2 variants of concern.
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Affiliation(s)
- Mengqi Yuan
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193 China
| | - Yanzhi Zhu
- College of Biological Sciences, China Agricultural University, Beijing, 100193 China
| | - Guanlan Liu
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193 China
| | - Yujie Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193 China
| | - Guanxi Wang
- College of Biological Sciences, China Agricultural University, Beijing, 100193 China
| | - Guozhong Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193 China
| | - Lilin Ye
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038 China
| | - Zhaohui Qian
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100176 China
| | - Pinghuang Liu
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193 China
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Li B, Guo J, Hu W, Chen Y. Binding affinity improvement analysis of multiple-mutant Omicron on 2019-nCov to human ACE2 by in silico predictions. J Mol Model 2023; 29:155. [PMID: 37093365 PMCID: PMC10123576 DOI: 10.1007/s00894-023-05536-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 03/01/2023] [Indexed: 04/25/2023]
Abstract
CONTEXT Since the outbreak of COVID-19 in 2019, the 2019-nCov coronavirus has appeared diverse mutational characteristics due to its own flexible conformation. One multiple-mutant strain (Omicron) with surprisingly infective activity outburst, and affected the biological activities of current drugs and vaccines, making the epidemic significantly difficult to prevent and control, and seriously threaten health around the world. Importunately exploration of mutant characteristics for novel coronavirus Omicron can supply strong theoretical guidance for learning binding mechanism of mutant viruses. What's more, full acknowledgement of key mutated-residues on Omicron strain can provide new methodology of the novel pathogenic mechanism to human ACE2 receptor, as well as the subsequent vaccine development. METHODS In this research, 3D structures of 32 single-point mutations of 2019-nCov were firstly constructed, and 32-sites multiple-mutant Omicron were finally obtained based one the wild-type virus by homology modeling method. One total number of 33 2019-nCov/ACE2 complex systems were acquired by protein-protein docking, and optimized by using preliminary molecular dynamic simulations. Binding free energies between each 2019-nCov mutation system and human ACE2 receptor were calculated, and corresponding binding patterns especially the regions adjacent to mutation site were analyzed. The results indicated that one total number of 6 mutated sites on the Omicron strain played crucial role in improving binding capacities from 2019-nCov to ACE2 protein. Subsequently, we performed long-term molecular dynamic simulations and protein-protein binding energy analysis for the selected 6 mutations. 3 infected individuals, the mutants T478K, Q493R and G496S with lower binding energies -66.36, -67.98 and -67.09 kcal/mol also presents the high infectivity. These findings indicated that the 3 mutations T478K, Q493R and G496S play the crucial roles in enhancing binding affinity of Omicron to human ACE2 protein. All these results illuminate important theoretical guidance for future virus detection of the Omicron epidemic, drug research and vaccine development.
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Affiliation(s)
- Bo Li
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Jindan Guo
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100021, China
| | - Wenxiang Hu
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan, 430205, China.
| | - Yubao Chen
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100021, China.
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Bao Y, He L, Miao B, Zhong Z, Lu G, Bai Y, Liang Q, Ling Y, Ji P, Su B, Zhao GP, Wu H, Zhang W, Wang Y, Chen Y, Xu J. BBIBP-CorV vaccination accelerates anti-viral antibody responses in heterologous Omicron infection: A retrospective observation study in Shanghai. Vaccine 2023; 41:3258-3265. [PMID: 37085449 DOI: 10.1016/j.vaccine.2023.03.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/23/2023]
Abstract
OBJECTIVES To investigate how BBIBP-CorV vaccination affecting antibody responses upon heterologous Omicron infection. METHODS 440 Omicron-infected patients were recruited in this study. Antibodies targeting SARS-CoV-2 spike protein receptor binding domain (RBD) and nucleoprotein of both wild-type (WT) and Omicron were detected by ELISA. The clinical relevance was further analyzed. RESULTS BBIBP-CorV vaccinated patients exhibited higher anti-RBD IgG levels targeting both WT and Omicron than non-vaccinated patients at different stages. By using a 3-day moving average analysis, we found that BBIBP-CorV vaccinated patients exhibited the increases in both anti-WT and Omicron RBD IgG from the onset and reached the plateau at Day 8 whereas those in non-vaccinated patients remained low during the disease. Significant increase in anti-WT RBD IgA was observed only in vaccinated patients. anti-Omicron RBD IgA levels remained low in both vaccinated and non-vaccinated patients. Clinically, severe COVID-19 only occurred in non-vaccinated group. anti-RBD IgG and IgA targeting both WT and Omicron were negatively correlated with virus load, hospitalization days and virus elimination in vaccinated patients. CONCLUSIONS BBIBP-CorV vaccination effectively reduces the severity of Omicron infected patients. The existence of humoral memory responses established through BBIBP-CorV vaccination facilitates to induce rapid recall antibody responses when encountering SARS-CoV-2 variant infection.
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Affiliation(s)
- Yujie Bao
- Department of Infectious Diseases, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Liheng He
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Benjie Miao
- Bio-Med Big Data Center, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhengrong Zhong
- Department of Clinical Diagnosis, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Guanzhu Lu
- Department of Infectious Diseases, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Yupan Bai
- Department of Infectious Diseases, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Qiming Liang
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yunchao Ling
- Bio-Med Big Data Center, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ping Ji
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Bing Su
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Guo-Ping Zhao
- Bio-Med Big Data Center, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hao Wu
- Department of Otorhinolaryngology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Wenhong Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai China
| | - Ying Wang
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases (20dz2261100), Shanghai 200025, China; Key Laboratory of Parasite and Vector Biology, Ministry of Health, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Yingying Chen
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Key Laboratory of Parasite and Vector Biology, Ministry of Health, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jie Xu
- Department of Infectious Diseases, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.
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Pan YY, Wang LC, Yang F, Yu M. Interferon-lambda: New role in intestinal symptoms of COVID-19. World J Gastroenterol 2023; 29:1942-1954. [PMID: 37155525 PMCID: PMC10122791 DOI: 10.3748/wjg.v29.i13.1942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/25/2022] [Accepted: 03/20/2023] [Indexed: 04/06/2023] Open
Abstract
The tremendous public health and economic impact of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a huge challenge globally. There is increasing evidence that SARS-CoV-2 induces intestinal infections. Type III interferon (IFN-λ) has an antiviral role in intestinal infection, with focused, long-lasting, and non-inflammatory characteristics. This review presents a summary of the structure of SARS-CoV-2, including its invasion and immune escape mechanisms. Emphasis was placed on the gastrointestinal impact of SARS-CoV-2, including changes to the intestinal microbiome, activation of immune cells, and inflammatory responses. We also describe the comprehensive functions of IFN-λ in anti-enteric SARS-CoV-2 infection, and discuss the potential application of IFN-λ as a therapeutic agent for COVID-19 with intestinal symptoms.
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Affiliation(s)
- Yi-Yang Pan
- Department of General Surgery, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Liu-Can Wang
- Department of General Surgery, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Feng Yang
- Department of General Surgery, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Min Yu
- Department of General Surgery, Chongqing General Hospital, Chongqing 400013, China
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Hariharan VN, Shin M, Chang CW, O’Reilly D, Biscans A, Yamada K, Guo Z, Somasundaran M, Tang Q, Monopoli K, Krishnamurthy PM, Devi G, McHugh N, Cooper DA, Echeverria D, Cruz J, Chan IL, Liu P, Lim SY, McConnell J, Singh SP, Hildebrand S, Sousa J, Davis SM, Kennedy Z, Ferguson C, Godinho BMDC, Thillier Y, Caiazzi J, Ly S, Muhuri M, Kelly K, Humphries F, Cousineau A, Parsi KM, Li Q, Wang Y, Maehr R, Gao G, Korkin D, McDougall WM, Finberg RW, Fitzgerald KA, Wang JP, Watts JK, Khvorova A. Divalent siRNAs are bioavailable in the lung and efficiently block SARS-CoV-2 infection. Proc Natl Acad Sci U S A 2023; 120:e2219523120. [PMID: 36893269 PMCID: PMC10089225 DOI: 10.1073/pnas.2219523120] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/05/2023] [Indexed: 03/11/2023] Open
Abstract
The continuous evolution of SARS-CoV-2 variants complicates efforts to combat the ongoing pandemic, underscoring the need for a dynamic platform for the rapid development of pan-viral variant therapeutics. Oligonucleotide therapeutics are enhancing the treatment of numerous diseases with unprecedented potency, duration of effect, and safety. Through the systematic screening of hundreds of oligonucleotide sequences, we identified fully chemically stabilized siRNAs and ASOs that target regions of the SARS-CoV-2 genome conserved in all variants of concern, including delta and omicron. We successively evaluated candidates in cellular reporter assays, followed by viral inhibition in cell culture, with eventual testing of leads for in vivo antiviral activity in the lung. Previous attempts to deliver therapeutic oligonucleotides to the lung have met with only modest success. Here, we report the development of a platform for identifying and generating potent, chemically modified multimeric siRNAs bioavailable in the lung after local intranasal and intratracheal delivery. The optimized divalent siRNAs showed robust antiviral activity in human cells and mouse models of SARS-CoV-2 infection and represent a new paradigm for antiviral therapeutic development for current and future pandemics.
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Affiliation(s)
- Vignesh N. Hariharan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Minwook Shin
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Ching-Wen Chang
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Daniel O’Reilly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Ken Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Zhiru Guo
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Mohan Somasundaran
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Qi Tang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Kathryn Monopoli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | | | - Gitali Devi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - David A. Cooper
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - John Cruz
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Io Long Chan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Ping Liu
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Sun-Young Lim
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jill McConnell
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Satya Prakash Singh
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Samuel Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jacquelyn Sousa
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Sarah M. Davis
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Zachary Kennedy
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Chantal Ferguson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Bruno M. D. C. Godinho
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Yann Thillier
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jillian Caiazzi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Socheata Ly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Manish Muhuri
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Karen Kelly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Fiachra Humphries
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Alyssa Cousineau
- Diabetes Center of Excellence and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Krishna Mohan Parsi
- Diabetes Center of Excellence and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Qi Li
- MassBiologics, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Yang Wang
- MassBiologics, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - René Maehr
- Diabetes Center of Excellence and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Guangping Gao
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA01655
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Dmitry Korkin
- Department of Computer Science, and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA01609
| | - William M. McDougall
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Robert W. Finberg
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Katherine A. Fitzgerald
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jennifer P. Wang
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jonathan K. Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
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Rabaan AA, Al-Ahmed SH, Albayat H, Alwarthan S, Alhajri M, Najim MA, AlShehail BM, Al-Adsani W, Alghadeer A, Abduljabbar WA, Alotaibi N, Alsalman J, Gorab AH, Almaghrabi RS, Zaidan AA, Aldossary S, Alissa M, Alburaiky LM, Alsalim FM, Thakur N, Verma G, Dhawan M. Variants of SARS-CoV-2: Influences on the Vaccines' Effectiveness and Possible Strategies to Overcome Their Consequences. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:507. [PMID: 36984508 PMCID: PMC10051174 DOI: 10.3390/medicina59030507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023]
Abstract
The immune response elicited by the current COVID-19 vaccinations declines with time, especially among the immunocompromised population. Furthermore, the emergence of novel SARS-CoV-2 variants, particularly the Omicron variant, has raised serious concerns about the efficacy of currently available vaccines in protecting the most vulnerable people. Several studies have reported that vaccinated people get breakthrough infections amid COVID-19 cases. So far, five variants of concern (VOCs) have been reported, resulting in successive waves of infection. These variants have shown a variable amount of resistance towards the neutralising antibodies (nAbs) elicited either through natural infection or the vaccination. The spike (S) protein, membrane (M) protein, and envelope (E) protein on the viral surface envelope and the N-nucleocapsid protein in the core of the ribonucleoprotein are the major structural vaccine target proteins against COVID-19. Among these targets, S Protein has been extensively exploited to generate effective vaccines against COVID-19. Hence, amid the emergence of novel variants of SARS-CoV-2, we have discussed their impact on currently available vaccines. We have also discussed the potential roles of S Protein in the development of novel vaccination approaches to contain the negative consequences of the variants' emergence and acquisition of mutations in the S Protein of SARS-CoV-2. Moreover, the implications of SARS-CoV-2's structural proteins were also discussed in terms of their variable potential to elicit an effective amount of immune response.
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Affiliation(s)
- Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Shamsah H. Al-Ahmed
- Specialty Paediatric Medicine, Qatif Central Hospital, Qatif 32654, Saudi Arabia
| | - Hawra Albayat
- Infectious Disease Department, King Saud Medical City, Riyadh 7790, Saudi Arabia
| | - Sara Alwarthan
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Mashael Alhajri
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Mustafa A. Najim
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Madinah 41411, Saudi Arabia
| | - Bashayer M. AlShehail
- Pharmacy Practice Department, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Wasl Al-Adsani
- Department of Medicine, Infectious Diseases Hospital, Kuwait City 63537, Kuwait
- Department of Infectious Diseases, Hampton Veterans Administration Medical Center, Hampton, VA 23667, USA
| | - Ali Alghadeer
- Department of Anesthesia, Dammam Medical Complex, Dammam 32245, Saudi Arabia
| | - Wesam A. Abduljabbar
- Department of Medical Laboratory Sciences, Fakeeh College for Medical Science, Jeddah 21134, Saudi Arabia
| | - Nouf Alotaibi
- Clinical Pharmacy Department, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Jameela Alsalman
- Infection Disease Unit, Department of Internal Medicine, Salmaniya Medical Complex, Ministry of Health, Kingdom of Bahrain, Manama 435, Bahrain
| | - Ali H. Gorab
- Al Kuzama Primary Health Care Center, Al Khobar Health Network, Eastern Health Cluster, Al Khobar 34446, Saudi Arabia
| | - Reem S. Almaghrabi
- Organ Transplant Center of Excellence, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Ali A. Zaidan
- Gastroenterology Department, King Fahad Armed Forces Hospital, Jeddah 23831, Saudi Arabia
| | - Sahar Aldossary
- Pediatric Infectious Diseases, Women and Children’s Health Institute, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Lamees M. Alburaiky
- Pediatric Department, Safwa General Hospital, Eastern Health Cluster, Safwa 31921, Saudi Arabia
| | - Fatimah Mustafa Alsalim
- Department of Family Medicine, Primary Health Care, Qatif Health Cluster, Qatif 32434, Saudi Arabia
| | - Nanamika Thakur
- University Institute of Biotechnology, Department of Biotechnology, Chandigarh University, Mohali 140413, India
| | - Geetika Verma
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana 141004, India
- Trafford College, Altrincham, Manchester WA14 5PQ, UK
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45
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Leonidou N, Renz A, Mostolizadeh R, Dräger A. New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells. PLoS Comput Biol 2023; 19:e1010903. [PMID: 36952396 PMCID: PMC10035753 DOI: 10.1371/journal.pcbi.1010903] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/30/2023] [Indexed: 03/25/2023] Open
Abstract
COVID-19 is one of the deadliest respiratory diseases, and its emergence caught the pharmaceutical industry off guard. While vaccines have been rapidly developed, treatment options for infected people remain scarce, and COVID-19 poses a substantial global threat. This study presents a novel workflow to predict robust druggable targets against emerging RNA viruses using metabolic networks and information of the viral structure and its genome sequence. For this purpose, we implemented pymCADRE and PREDICATE to create tissue-specific metabolic models, construct viral biomass functions and predict host-based antiviral targets from more than one genome. We observed that pymCADRE reduces the computational time of flux variability analysis for internal optimizations. We applied these tools to create a new metabolic network of primary bronchial epithelial cells infected with SARS-CoV-2 and identified enzymatic reactions with inhibitory effects. The most promising reported targets were from the purine metabolism, while targeting the pyrimidine and carbohydrate metabolisms seemed to be promising approaches to enhance viral inhibition. Finally, we computationally tested the robustness of our targets in all known variants of concern, verifying our targets' inhibitory effects. Since laboratory tests are time-consuming and involve complex readouts to track processes, our workflow focuses on metabolic fluxes within infected cells and is applicable for rapid hypothesis-driven identification of potentially exploitable antivirals concerning various viruses and host cell types.
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Affiliation(s)
- Nantia Leonidou
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karls University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard Karls University of Tübingen, Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Alina Renz
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karls University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard Karls University of Tübingen, Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Reihaneh Mostolizadeh
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karls University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard Karls University of Tübingen, Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, Eberhard Karls University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Germany
| | - Andreas Dräger
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karls University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard Karls University of Tübingen, Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, Eberhard Karls University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Germany
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46
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Hillary VE, Ceasar SA. An update on COVID-19: SARS-CoV-2 variants, antiviral drugs, and vaccines. Heliyon 2023; 9:e13952. [PMID: 36855648 PMCID: PMC9946785 DOI: 10.1016/j.heliyon.2023.e13952] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/07/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly contagious and pathogenic virus that first appeared in late December 2019. This SARS-CoV-2 causes an infection of an acute respiratory disease called "coronavirus infectious disease-2019 (COVID-19). The World Health Organization (WHO) declared this SARS-CoV-2 outbreak a great pandemic on March 11, 2020. As of January 31, 2023, SARS-CoV-2 recorded more than 67 million cases and over 6 million deaths. Recently, novel mutated variants of SARS-CoV are also creating a serious health concern worldwide, and the future novel variant is still mysterious. As infection cases of SARS-CoV-2 are increasing daily, scientists are trying to combat the disease using numerous antiviral drugs and vaccines against SARS-CoV-2. To our knowledge, this is the first comprehensive review that summarized the dynamic nature of SARS-CoV-2 transmission, SARS-CoV-2 variants (a variant of concern and variant of interest), antiviral drugs and vaccines utilized against SARS-CoV-2 at a glance. Hopefully, this review will enable the researcher to gain knowledge on SARS-CoV-2 variants and vaccines, which will also pave the way to identify efficient novel vaccines against forthcoming SARS-CoV-2 strains.
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Key Words
- ACE2, Angiotensin-converting enzyme 2
- Antiviral drugs
- COVID-19
- COVID-19, Coronavirus infectious disease-2019
- EUA, Emergency Use Authorization
- FDA, Food and Drug Administration
- NIH, National Institutes of Health
- RBD, Receptor-binding domain
- SARS-CoV-2
- SARS-CoV-2 variants
- SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2
- VOC, Variants of Concern
- VOI, Variants of Interests
- Vaccines
- WHO, World Health Organization
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Affiliation(s)
- Varghese Edwin Hillary
- Department of Biosciences, Rajagiri College of Social Sciences, Cochin, 683 104, Kerala, India
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47
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Lanyon HE, Hoyle JS, Downard KM. Resolving omicron sub-variants of SARS CoV-2 coronavirus with MALDI mass spectrometry. Analyst 2023; 148:966-972. [PMID: 36757162 DOI: 10.1039/d2an01843h] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Mass mapping using high resolution mass spectrometry has been applied to identify and rapidly distinguish the omicron sub-variants across the BA.1-BA.5 lineages. Lineage-specific protein mutations in the surface spike protein give rise to peptide biomarkers of unique mass that can be confidently and sensitively detected with high resolution mass spectrometry. Those that are most efficiently ionised and detected within the S1 subunit in recombinant forms facilitate their detection in clinical specimens containing other SARS-CoV2 viral proteins and contaminants. A study of five dozen omicron-positive specimens, using a selected ion monitoring approach, detected peptide biomarkers for strains of BA.1, BA.2.75 and BA.4 sub-variants in 23%, 42% and 28% of samples respectively, consistent with their reported levels in the local population. The virus was confidently assigned in over 93% of omicron positive specimens. The ease of detection of the BA.2.75 variant, in particular, is of vital importance given its rapid global spread in late 2022 due to several immune evasive mutations within the receptor-binding domain.
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Affiliation(s)
- Henry E Lanyon
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, Australia.
| | - Joshua S Hoyle
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, Australia.
| | - Kevin M Downard
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, Australia.
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48
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SARS-CoV-2 versus Influenza A Virus: Characteristics and Co-Treatments. Microorganisms 2023; 11:microorganisms11030580. [PMID: 36985154 PMCID: PMC10051779 DOI: 10.3390/microorganisms11030580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
For three years, the novel coronavirus disease 2019 (COVID-19) pandemic, caused by infection of the SARS-CoV-2 virus, has completely changed our lifestyles and prepared us to live with this novel pneumonia for years to come. Given that pre-existing flu is caused by the influenza A virus, we have begun unprecedently co-coping with two different respiratory diseases at the same time. Hence, we draw a comparison between SARS-CoV-2 and influenza A virus based on the general characteristics, especially the main variants’ history and the distribution of the two viruses. SARS-CoV-2 appeared to mutate more frequently and independently of locations than the influenza A virus. Furthermore, we reviewed present clinical trials on combined management against COVID-19 and influenza in order to explore better solutions against both at the same time.
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49
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Hattab D, Amer MFA, Mohd Gazzali A, Chuah LH, Bakhtiar A. Current status in cellular-based therapies for prevention and treatment of COVID-19. Crit Rev Clin Lab Sci 2023:1-25. [PMID: 36825325 DOI: 10.1080/10408363.2023.2177605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the pathogen responsible for the coronavirus disease 2019 (COVID-19) outbreaks that resulted in a catastrophic threat to global health, with more than 500 million cases detected and 5.5 million deaths worldwide. Patients with a COVID-19 infection presented with clinical manifestations ranging from asymptomatic to severe symptoms, resulting in acute lung injury, acute respiratory distress syndrome, and even death. Immune dysregulation through delayed innate immune response or impairment of the adaptive immune response is the key contributor to the pathophysiology of COVID-19 and SARS-CoV-2-induced cytokine storm. Symptomatic and supportive therapy is the fundamental strategy in treating COVID-19 infection, including antivirals, steroid-based therapies, and cell-based immunotherapies. Various studies reported substantial effects of immune-based therapies for patients with COVID-19 to modulate the over-activated immune system while simultaneously refining the body's ability to destroy the virus. However, challenges may arise from the complexity of the disease through the genetic variance of the virus itself and patient heterogeneity, causing increased transmissibility and heightened immune system evasion that rapidly change the intervention and prevention measures for SARS-CoV-2. Cell-based therapy, utilizing stem cells, dendritic cells, natural killer cells, and T cells, among others, are being extensively explored as other potential immunological approaches for preventing and treating SARS-CoV-2-affected patients the similar process was effectively proven in SARS-CoV-1 and MERS-CoV infections. This review provides detailed insights into the innate and adaptive immune response-mediated cell-based immunotherapies in COVID-19 patients. The immune response linking towards engineered autologous or allogenic immune cells for either treatment or preventive therapies is subsequently highlighted in an individual study or in combination with several existing treatments. Up-to-date data on completed and ongoing clinical trials of cell-based agents for preventing or treating COVID-19 are also outlined to provide a guide that can help in treatment decisions and future trials.
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Affiliation(s)
- Dima Hattab
- Faculty of Pharmacy, Al-Ahliyya Amman University, Amman, Jordan
| | - Mumen F A Amer
- Faculty of Pharmacy, Applied Science Private University, Amman, Jordan
| | - Amirah Mohd Gazzali
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Lay Hong Chuah
- School of Pharmacy, Monash University Malaysia, Selangor, Malaysia
| | - Athirah Bakhtiar
- School of Pharmacy, Monash University Malaysia, Selangor, Malaysia
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50
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Katuwal S, Upadhyaya SR, Marahatha R, Shrestha A, Regmi BP, Khadayat K, Basnet S, Basnyat RC, Parajuli N. In Silico Study of Coumarins: Wedelolactone as a Potential Inhibitor of the Spike Protein of the SARS-CoV-2 Variants. J Trop Med 2023; 2023:4771745. [PMID: 39262685 PMCID: PMC11390206 DOI: 10.1155/2023/4771745] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/20/2022] [Accepted: 01/24/2023] [Indexed: 09/13/2024] Open
Abstract
Despite the rigorous global efforts to control SARS-CoV-2 transmission, it continues to pose a serious threat to humans with the frequent emergence of new variants. Thus, robust therapeutics to combat the virus are a desperate need. The SARS-CoV-2 spike (S) protein is an important target protein as it mediates the entry of the virus inside the host cells, which is initiated by the binding of the receptor-binding domain (RBD) to its cognate receptor, angiotensin-converting enzyme 2 (ACE-2). Herein, the inhibition potential of several naturally occurring coumarins was investigated against the spike proteins of SARS-CoV-2 variants using computational approaches. Molecular docking studies revealed 26 coumarins with better binding energies than the reference ligands, molnupiravir and ceftazidime, against the S-RBD of the omicron variant. The top 10 best-docked coumarins were further analyzed to understand their binding interactions against the spike proteins of other variants (wild-type, Alpha, Beta, Gamma, and Delta), and these studies also demonstrated decent binding energies. Physicochemical, QSAR, and pharmacokinetics analyses of the coumarins revealed wedelolactone as the best inhibitor of the spike protein with ideal Lipinski's drug-likeness and optimal ADMET properties. Furthermore, coarse-grained molecular dynamics (MD) simulation studies of spike protein-wedelolactone complexes validated the stable binding of wedelolactone in the respective binding pockets. As an outcome, wedelolactone could be utilized to develop a potent drug candidate against COVID-19 by blocking the viral entry into the host cell.
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Affiliation(s)
- Saurav Katuwal
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Siddha Raj Upadhyaya
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Rishab Marahatha
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Asmita Shrestha
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Bishnu P Regmi
- Department of Chemistry, Florida Agricultural and Mechanical University, Tallahassee, FL 32307, USA
| | - Karan Khadayat
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Saroj Basnet
- Center for Drug Design and Molecular Simulation Division, Cancer Care and Research Center, Kathmandu, Nepal
| | - Ram Chandra Basnyat
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Niranjan Parajuli
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
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