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Shum MHH, Lee Y, Tam L, Xia H, Chung OLW, Guo Z, Lam TTY. Binding affinity between coronavirus spike protein and human ACE2 receptor. Comput Struct Biotechnol J 2024; 23:759-770. [PMID: 38304547 PMCID: PMC10831124 DOI: 10.1016/j.csbj.2024.01.009] [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: 09/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Coronaviruses (CoVs) pose a major risk to global public health due to their ability to infect diverse animal species and potential for emergence in humans. The CoV spike protein mediates viral entry into the cell and plays a crucial role in determining the binding affinity to host cell receptors. With particular emphasis on α- and β-coronaviruses that infect humans and domestic animals, current research on CoV receptor use suggests that the exploitation of the angiotensin-converting enzyme 2 (ACE2) receptor poses a significant threat for viral emergence with pandemic potential. This review summarizes the approaches used to study binding interactions between CoV spike proteins and the human ACE2 (hACE2) receptor. Solid-phase enzyme immunoassays and cell binding assays allow qualitative assessment of binding but lack quantitative evaluation of affinity. Surface plasmon resonance, Bio-layer interferometry, and Microscale Thermophoresis on the other hand, provide accurate affinity measurement through equilibrium dissociation constants (KD). In silico modeling predicts affinity through binding structure modeling, protein-protein docking simulations, and binding energy calculations but reveals inconsistent results due to the lack of a standardized approach. Machine learning and deep learning models utilize simulated and experimental protein-protein interaction data to elucidate the critical residues associated with CoV binding affinity to hACE2. Further optimization and standardization of existing approaches for studying binding affinity could aid pandemic preparedness. Specifically, prioritizing surveillance of CoVs that can bind to human receptors stands to mitigate the risk of zoonotic spillover.
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Affiliation(s)
- Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Yang Lee
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
| | - Leighton Tam
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Hui Xia
- Department of Chemistry, South University of Science and Technology of China, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Oscar Lung-Wa Chung
- Department of Chemistry, South University of Science and Technology of China, China
| | - Zhihong Guo
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2021-2022. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38925550 DOI: 10.1002/mas.21873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 06/28/2024]
Abstract
The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well-established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.
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Wang S, Ran W, Sun L, Fan Q, Zhao Y, Wang B, Yang J, He Y, Wu Y, Wang Y, Chen L, Chuchuay A, You Y, Zhu X, Wang X, Chen Y, Wang Y, Chen YQ, Yuan Y, Zhao J, Mao Y. Sequential glycosylations at the multibasic cleavage site of SARS-CoV-2 spike protein regulate viral activity. Nat Commun 2024; 15:4162. [PMID: 38755139 PMCID: PMC11099032 DOI: 10.1038/s41467-024-48503-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 04/30/2024] [Indexed: 05/18/2024] Open
Abstract
The multibasic furin cleavage site at the S1/S2 boundary of the spike protein is a hallmark of SARS-CoV-2 and plays a crucial role in viral infection. However, the mechanism underlying furin activation and its regulation remain poorly understood. Here, we show that GalNAc-T3 and T7 jointly initiate clustered O-glycosylations in the furin cleavage site of the SARS-CoV-2 spike protein, which inhibit furin processing, suppress the incorporation of the spike protein into virus-like-particles and affect viral infection. Mechanistic analysis reveals that the assembly of the spike protein into virus-like particles relies on interactions between the furin-cleaved spike protein and the membrane protein of SARS-CoV-2, suggesting a possible mechanism for furin activation. Interestingly, mutations in the spike protein of the alpha and delta variants of the virus confer resistance against glycosylation by GalNAc-T3 and T7. In the omicron variant, additional mutations reverse this resistance, making the spike protein susceptible to glycosylation in vitro and sensitive to GalNAc-T3 and T7 expression in human lung cells. Our findings highlight the role of glycosylation as a defense mechanism employed by host cells against SARS-CoV-2 and shed light on the evolutionary interplay between the host and the virus.
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Affiliation(s)
- Shengjun Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, China
| | - Wei Ran
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lingyu Sun
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qingchi Fan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuanqi Zhao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Foshan Institute for Food and Drug Control, Foshan, China
| | - Bowen Wang
- College of Life Science, Northwest University, Xi'an, China
| | - Jinghong Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuqi He
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuanyuan Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Luoyi Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Arpaporn Chuchuay
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuyu You
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xinhai Zhu
- Instrumental Analysis & Research Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaojuan Wang
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ye Chen
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yanqiu Yuan
- State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, China.
- Guangzhou Laboratory, Bio-island, Guangzhou, China.
- The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China.
| | - Yang Mao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Drug Non-Clinical Evaluation and Research, Guangzhou, China.
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Schwarze M, Volke D, Rojas Echeverri JC, Schick R, Lakowa N, Grünewald T, Wolf J, Borte S, Scholz M, Krizsan A, Hoffmann R. Influence of Mutations and N-Glycosylation Sites in the Receptor-Binding Domain (RBD) and the Membrane Protein of SARS-CoV-2 Variants of Concern on Antibody Binding in ELISA. BIOLOGY 2024; 13:207. [PMID: 38666819 PMCID: PMC11047955 DOI: 10.3390/biology13040207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect human cells by first attaching to the ACE-2 receptor via its receptor-binding domain (RBD) in the spike protein. Here, we report the influence of N-glycosylation sites of the RBD and the membrane (M) protein on IgG antibody binding in serum samples from patients infected with the original SARS-CoV-2 strain in Germany. The RBDs of the wildtype, alpha, beta, gamma, and kappa variants expressed in HEK293S GnTI- cells were all N-glycosylated at Asn331, Asn334, Asn343, and Asn360 or Asn370, whereas the M-protein was glycosylated at Asn5. An ELISA using a coated RBD and probed with anti-RBD IgG antibodies gave a sensitivity of 96.3% and a specificity of 100% for the wildtype RBD, while the sensitivity decreased by 5% to 10% for the variants of concern, essentially in the order of appearance. Deglycosylation of the wildtype RBD strongly reduced antibody recognition by ~20%, considering the mean of the absorbances recorded for the ELISA. This effect was even stronger for the unglycosylated RBD expressed in Escherichia coli, suggesting structural changes affecting epitope recognition. Interestingly, the N-glycosylated M-protein expressed in HEK293S GnTI- cells gave good sensitivity (95%), which also decreased to 65% after deglycosylation, and selectivity (100%). In conclusion, N-glycosylation of the M-protein, the RBD, and most likely the spike protein are important for proper antibody binding and immunological assays, whereas the type of N-glycosylation is less relevant.
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Affiliation(s)
- Mandy Schwarze
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany; (M.S.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04103 Leipzig, Germany
| | - Daniela Volke
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany; (M.S.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04103 Leipzig, Germany
| | - Juan Camilo Rojas Echeverri
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany; (M.S.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04103 Leipzig, Germany
| | - Robin Schick
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany; (M.S.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04103 Leipzig, Germany
| | - Nicole Lakowa
- Klinik für Infektions- und Tropenmedizin, Klinikum Chemnitz gGmbH, 09113 Chemnitz, Germany (T.G.)
| | - Thomas Grünewald
- Klinik für Infektions- und Tropenmedizin, Klinikum Chemnitz gGmbH, 09113 Chemnitz, Germany (T.G.)
| | - Johannes Wolf
- Department of Laboratory Medicine, Hospital St. Georg gGmbH, 04129 Leipzig, Germany
- Immuno Deficiency Center Leipzig, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiency Diseases, Hospital St. Georg gGmbH, 04129 Leipzig, Germany
| | - Stephan Borte
- Department of Laboratory Medicine, Hospital St. Georg gGmbH, 04129 Leipzig, Germany
- Immuno Deficiency Center Leipzig, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiency Diseases, Hospital St. Georg gGmbH, 04129 Leipzig, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, Universität Leipzig, 04107 Leipzig, Germany
- LIFE Research Center of Civilization Diseases, Universität Leipzig, 04103 Leipzig, Germany
| | - Andor Krizsan
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany; (M.S.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04103 Leipzig, Germany
| | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany; (M.S.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04103 Leipzig, Germany
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5
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Wei L, Chen Y, Feng X, Yao J, Zhang L, Zhou X, Yan G, Qiu H, Wang C, Lu H. Elucidation of N-/ O-glycosylation and site-specific mapping of sialic acid linkage isomers of SARS-CoV-2 human receptor angiotensin-converting enzyme 2. Analyst 2023; 148:5002-5011. [PMID: 37728433 DOI: 10.1039/d3an01079a] [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: 09/21/2023]
Abstract
Human angiotensin-converting enzyme 2 (hACE2) is the primary receptor for cellular entry of SARS-CoV-2 into human host cells. hACE2 is heavily glycosylated and glycans on the receptor may play a role in viral binding. Thus, comprehensive characterization of hACE2 glycosylation could aid our understanding of interactions between the receptor and SARS-CoV-2 spike (S) protein, as well as provide a basis for the development of therapeutic drugs targeting this crucial interaction. Herein, 138 N-glycan compositions were identified, most of which are complex-type N-glycans, from seven N-glycosites of hACE2. Among them, 67% contain at least one sialic acid residue. At the level of glycopeptides, the overall quantification of sialylated glycan isomers observed on the sites N322 and N546 have a higher degree of NeuAc (α2-3)Gal (over 80.3%) than that of other N-glycosites (35.6-71.0%). In terms of O-glycans, 69 glycan compositions from 12 O-glycosites were identified, and especially, the C-terminus of hACE2 is heavily O-glycosylated. The terminal sialic acid linkage type of H1N1S1 and H1N1S2 are covered highly with α2,3-sialic acid. These findings could aid the investigation of the interaction between SARS-CoV-2 and human host cells.
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Affiliation(s)
- Liming Wei
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, 131 Dongan Road, 20032 Shanghai, China.
| | - Yuning Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences Department, 555 Zuchongzhi Road, 201203 Shanghai, China.
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, 100049 Beijing, China
| | - Xiaoxiao Feng
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, 131 Dongan Road, 20032 Shanghai, China.
| | - Jun Yao
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, 131 Dongan Road, 20032 Shanghai, China.
| | - Lei Zhang
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, 131 Dongan Road, 20032 Shanghai, China.
| | - Xinwen Zhou
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, 131 Dongan Road, 20032 Shanghai, China.
| | - Guoquan Yan
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, 131 Dongan Road, 20032 Shanghai, China.
| | - Hong Qiu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences Department, 555 Zuchongzhi Road, 201203 Shanghai, China.
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, 100049 Beijing, China
| | - Chunhe Wang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences Department, 555 Zuchongzhi Road, 201203 Shanghai, China.
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, 100049 Beijing, China
| | - Haojie Lu
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, 131 Dongan Road, 20032 Shanghai, China.
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Reyes CDG, Onigbinde S, Sanni A, Bennett AI, Jiang P, Daramola O, Ahmadi P, Fowowe M, Atashi M, Sandilya V, Hakim MA, Mechref Y. N-Glycome Profile of the Spike Protein S1: Systemic and Comparative Analysis from Eleven Variants of SARS-CoV-2. Biomolecules 2023; 13:1421. [PMID: 37759821 PMCID: PMC10526240 DOI: 10.3390/biom13091421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/01/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
The SARS-CoV-2 virus rapidly spread worldwide, threatening public health. Since it emerged, the scientific community has been engaged in the development of effective therapeutics and vaccines. The subunit S1 in the spike protein of SARS-CoV-2 mediates the viral entry into the host and is therefore one of the major research targets. The S1 protein is extensively glycosylated, and there is compelling evidence that glycans protect the virus' active site from the human defense system. Therefore, investigation of the S1 protein glycome alterations in the different virus variants will provide a view of the glycan evolution and its relationship with the virus pathogenesis. In this study, we explored the N-glycosylation expression of the S1 protein for eleven SARS-CoV-2 variants: five variants of concern (VOC), including alpha, beta, gamma, delta, and omicron, and six variants of interest (VOI), including epsilon, eta, iota, lambda, kappa, and mu. The results showed significant differences in the N-glycome abundance of all variants. The N-glycome of the VOC showed a large increase in the abundance of sialofucosylated glycans, with the greatest abundance in the omicron variant. In contrast, the results showed a large abundance of fucosylated glycans for most of the VOI. Two glycan compositions, GlcNAc4,Hex5,Fuc,NeuAc (4-5-1-1) and GlcNAc6,Hex8,Fuc,NeuAc (6-8-1-1), were the most abundant structures across all variants. We believe that our data will contribute to understanding the S1 protein's structural differences between SARS-CoV-2 mutations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (C.D.G.R.); (S.O.); (A.S.); (A.I.B.); (P.J.); (O.D.); (P.A.); (M.F.); (M.A.); (V.S.); (M.A.H.)
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7
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Sung JCC, Wu PL, So EYM, Wu KC, Chan SMN, Kwong KWY, Sze ETP. Assessment of novel antiviral filter using pseudo-type SARS-CoV-2 virus in fast air velocity vertical-type wind tunnel. Sci Rep 2023; 13:13947. [PMID: 37626166 PMCID: PMC10457382 DOI: 10.1038/s41598-023-41245-8] [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: 06/06/2023] [Accepted: 08/23/2023] [Indexed: 08/27/2023] Open
Abstract
Current evidence suggests that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can remain suspended spread in aerosols for longer period of time under poorly ventilated indoor setting. To minimize spreading, application of antiviral filter to capture infectious aerosols and to inactivate SARS-CoV-2 can be a promising solution. This study aimed to develop a method to assess simultaneously the filtration and removal efficiency of aerosolized pseudo-type SARS-CoV-2 using a vertical-type wind tunnel with relatively high face velocity (1.3 m/s). Comparing with the untreated spunlace non-woven filter, the C-POLAR™ treated filter increased the filtration efficiency from 74.2 ± 11.5% to 97.2 ± 1.7%, with the removal efficiency of 99.4 ± 0.051%. The results provided not only solid evidence to support the effectiveness of the cationic polymeric coated filter in fighting against the SARS-CoV-2 pandemic, but also a method to test viral filtration and removal efficiency under relative fast air velocity and with a safer environment to the operators.
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Affiliation(s)
| | - Pak-Long Wu
- School of Science and Technology, Hong Kong Metropolitan University, Hong Kong, China
| | - Ellis Yung-Mau So
- School of Science and Technology, Hong Kong Metropolitan University, Hong Kong, China
| | - Kam-Chau Wu
- Research Department, DreamTec Cytokines Limited, Hong Kong, China
| | - Sidney Man-Ngai Chan
- School of Science and Technology, Hong Kong Metropolitan University, Hong Kong, China
| | | | - Eric Tung-Po Sze
- School of Science and Technology, Hong Kong Metropolitan University, Hong Kong, China.
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8
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Franco EJ, Drusano GL, Hanrahan KC, Warfield KL, Brown AN. Combination Therapy with UV-4B and Molnupiravir Enhances SARS-CoV-2 Suppression. Viruses 2023; 15:v15051175. [PMID: 37243261 DOI: 10.3390/v15051175] [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: 04/25/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
The host targeting antiviral, UV-4B, and the RNA polymerase inhibitor, molnupiravir, are two orally available, broad-spectrum antivirals that have demonstrated potent activity against SARS-CoV-2 as monotherapy. In this work, we evaluated the effectiveness of UV-4B and EIDD-1931 (molnupiravir's main circulating metabolite) combination regimens against the SARS-CoV-2 beta, delta, and omicron BA.2 variants in a human lung cell line. Infected ACE2 transfected A549 (ACE2-A549) cells were treated with UV-4B and EIDD-1931 both as monotherapy and in combination. Viral supernatant was sampled on day three when viral titers peaked in the no-treatment control arm, and levels of infectious virus were measured by plaque assay. The drug-drug effect interaction between UV-4B and EIDD-1931 was also defined using the Greco Universal Response Surface Approach (URSA) model. Antiviral evaluations demonstrated that treatment with UV-4B plus EIDD-1931 enhanced antiviral activity against all three variants relative to monotherapy. These results were in accordance with those obtained from the Greco model, as these identified the interaction between UV-4B and EIDD-1931 as additive against the beta and omicron variants and synergistic against the delta variant. Our findings highlight the anti-SARS-CoV-2 potential of UV-4B and EIDD-1931 combination regimens, and present combination therapy as a promising therapeutic strategy against SARS-CoV-2.
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Affiliation(s)
- Evelyn J Franco
- Institute for Therapeutic Innovation, Department of Medicine, College of Medicine, University of Florida, Orlando, FL 32827, USA
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando, FL 32827, USA
| | - George L Drusano
- Institute for Therapeutic Innovation, Department of Medicine, College of Medicine, University of Florida, Orlando, FL 32827, USA
| | - Kaley C Hanrahan
- Institute for Therapeutic Innovation, Department of Medicine, College of Medicine, University of Florida, Orlando, FL 32827, USA
| | | | - Ashley N Brown
- Institute for Therapeutic Innovation, Department of Medicine, College of Medicine, University of Florida, Orlando, FL 32827, USA
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando, FL 32827, USA
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9
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Harless WW, Lewis B, Qorri B, Abdulkhalek S, Szewczuk MR. Novel Therapeutic Target Critical for SARS-CoV-2 Infectivity and Induction of the Cytokine Release Syndrome. Cells 2023; 12:cells12091332. [PMID: 37174732 PMCID: PMC10177205 DOI: 10.3390/cells12091332] [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: 02/02/2023] [Revised: 04/21/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
We discovered a novel therapeutic target critical for SARS-CoV-2, cellular infectivity and the induction of the cytokine release syndrome. Here, we show that the mammalian enzyme neuraminidase-1 (Neu-1) is part of a highly conserved signaling platform that regulates the dimerization and activation of the ACE2 receptors and the Toll-like receptors (TLRs) implicated in the cytokine release syndrome (CRS). Activated Neu-1 cleaves glycosylated residues that provide a steric hindrance to both ACE2 and TLR dimerization, a process critical to both viral attachment to the receptor and entry into the cell and TLR activation. Blocking Neu-1 inhibited ACE2 receptor dimerization and internalization, TLR dimerization and activation, and the expression of several key inflammatory molecules implicated in the CRS and death from ARDS. Treatments that target Neu-1 are predicted to be highly effective against infection with SARS-CoV-2, given the central role played by this enzyme in viral cellular entry and the induction of the CRS.
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Affiliation(s)
| | - Beth Lewis
- ENCYT Technologies Inc., Membertou, NS B1S 0H1, Canada
| | - Bessi Qorri
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Samar Abdulkhalek
- Faculty of Health Sciences, Higher Colleges of Technology, Abu Dhabi P.O. Box 25026, United Arab Emirates
| | - Myron R Szewczuk
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
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10
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Mironov AA, Savin MA, Beznoussenko GV. COVID-19 Biogenesis and Intracellular Transport. Int J Mol Sci 2023; 24:ijms24054523. [PMID: 36901955 PMCID: PMC10002980 DOI: 10.3390/ijms24054523] [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: 01/04/2023] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 03/02/2023] Open
Abstract
SARS-CoV-2 is responsible for the COVID-19 pandemic. The structure of SARS-CoV-2 and most of its proteins of have been deciphered. SARS-CoV-2 enters cells through the endocytic pathway and perforates the endosomes' membranes, and its (+) RNA appears in the cytosol. Then, SARS-CoV-2 starts to use the protein machines of host cells and their membranes for its biogenesis. SARS-CoV-2 generates a replication organelle in the reticulo-vesicular network of the zippered endoplasmic reticulum and double membrane vesicles. Then, viral proteins start to oligomerize and are subjected to budding within the ER exit sites, and its virions are passed through the Golgi complex, where the proteins are subjected to glycosylation and appear in post-Golgi carriers. After their fusion with the plasma membrane, glycosylated virions are secreted into the lumen of airways or (seemingly rarely) into the space between epithelial cells. This review focuses on the biology of SARS-CoV-2's interactions with cells and its transport within cells. Our analysis revealed a significant number of unclear points related to intracellular transport in SARS-CoV-2-infected cells.
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Affiliation(s)
- Alexander A. Mironov
- Department of Cell Biology, IFOM ETS—The AIRC Institute of Molecular Oncology, Via Adamello, 16, 20139 Milan, Italy
- Correspondence:
| | - Maksim A. Savin
- The Department for Welding Production and Technology of Constructional Materials, Perm National Research Polytechnic University, Komsomolsky Prospekt, 29, 614990 Perm, Russia
| | - Galina V. Beznoussenko
- Department of Cell Biology, IFOM ETS—The AIRC Institute of Molecular Oncology, Via Adamello, 16, 20139 Milan, Italy
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11
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Najeeb N, Murukan AB, Renjitha A, Jayaram M, Jabbar AA, Haridasan H, Prijikumar A, Baiju S, Nixon AA, Krishnan PA, Rodriguez S, Kumar S, Polipalli SK, Singh KK, Nair BG, Ghate SD, Rao RSP, Kishor PBK, Aloor A, Suravajhala R, Chaubey G, Suravajhala P. Inferring Recombination Events in SARS-CoV-2 Variants In Silico. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1412:253-270. [PMID: 37378772 DOI: 10.1007/978-3-031-28012-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Over the last 34 months, at least 10 severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) distinct variants have evolved. Among these, some were more infectious while others were not. These variants may serve as candidates for identification of the signature sequences linked to infectivity and viral transgressions. Based on our previous hijacking and transgression hypothesis, we aimed to investigate whether SARS-CoV-2 sequences associated with infectivity and trespassing of long noncoding RNAs (lncRNAs) provide a possible recombination mechanism to drive the formation of new variants. This work involved a sequence and structure-based approach to screen SARS-CoV-2 variants in silico, taking into account effects of glycosylation and links to known lncRNAs. Taken together, the findings suggest that transgressions involving lncRNAs may be linked with changes in SARS-CoV-2-host interactions driven by glycosylation events.
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Affiliation(s)
- Nihal Najeeb
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Aparna B Murukan
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Anagha Renjitha
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Malavika Jayaram
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Ayisha A Jabbar
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Haripriya Haridasan
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Akshara Prijikumar
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Sneha Baiju
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Adrial Ann Nixon
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | | | - Sunu Rodriguez
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Somesh Kumar
- Genome Sequencing Lab, Lok Nayak Hospital, Delhi, India
| | | | - Keshav K Singh
- Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Kaul Genetics Building, Birmingham, AL, USA
| | - Bipin G Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Sudeep D Ghate
- Center for Bioinformatics, NITTE University, Mangaluru, India
| | | | | | - Arya Aloor
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Renuka Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India.
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12
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Aloor A, Aradhya R, Venugopal P, Gopalakrishnan Nair B, Suravajhala R. Glycosylation in SARS-CoV-2 variants: A path to infection and recovery. Biochem Pharmacol 2022; 206:115335. [PMID: 36328134 PMCID: PMC9621623 DOI: 10.1016/j.bcp.2022.115335] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/25/2022] [Accepted: 10/25/2022] [Indexed: 11/05/2022]
Abstract
Glycan is an essential molecule that controls and drives life in a precise direction. The paucity of research in glycobiology may impede the significance of its role in the pandemic guidelines. The SARS-CoV-2 spike protein is heavily glycosylated, with 22 putative N-glycosylation sites and 17 potential O-glycosylation sites discovered thus far. It is the anchor point to the host cell ACE2 receptor, TMPRSS2, and many other host proteins that can be recognized by their immune system; hence, glycosylation is considered the primary target of vaccine development. Therefore, it is essential to know how this surface glycan plays a role in viral entry, infection, transmission, antigen, antibody responses, and disease progression. Although the vaccines are developed and applied against COVID-19, the proficiency of the immunizations is not accomplished with the current mutant variations. The role of glycosylation in SARS-CoV-2 and its receptor ACE2 with respect to other putative cell glycan receptors and the significance of glycan in host cell immunity in COVID-19 are discussed in this paper. Hence, the molecular signature of the glycan in the coronavirus infection can be incorporated into the mainstream therapeutic process.
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Affiliation(s)
- Arya Aloor
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana 690525, Kerala, India.
| | - Rajaguru Aradhya
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana 690525, Kerala, India.
| | - Parvathy Venugopal
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana 690525, Kerala, India.
| | | | - Renuka Suravajhala
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana 690525, Kerala, India.
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13
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Bayani F, Safaei Hashkavaei N, Uversky VN, Mozaffari-Jovin S, Sefidbakht Y. Insights into the structural peculiarities of the N-terminal and receptor binding domains of the spike protein from the SARS-CoV-2 Omicron variant. Comput Biol Med 2022; 147:105735. [PMID: 35767919 PMCID: PMC9220253 DOI: 10.1016/j.compbiomed.2022.105735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/26/2022] [Accepted: 06/11/2022] [Indexed: 11/03/2022]
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14
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Campos D, Girgis M, Sanda M. Site-specific glycosylation of SARS-CoV-2: Big challenges in mass spectrometry analysis. Proteomics 2022; 22:e2100322. [PMID: 35700310 PMCID: PMC9349404 DOI: 10.1002/pmic.202100322] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/03/2022] [Accepted: 06/13/2022] [Indexed: 12/24/2022]
Abstract
Glycosylation of viral proteins is required for the progeny formation and infectivity of virtually all viruses. It is increasingly clear that distinct glycans also play pivotal roles in the virus's ability to shield and evade the host's immune system. Recently, there has been a great advancement in structural identification and quantitation of viral glycosylation, especially spike proteins. Given the ongoing pandemic and the high demand for structure analysis of SARS-CoV-2 densely glycosylated spike protein, mass spectrometry methodologies have been employed to accurately determine glycosylation patterns. There are still many challenges in the determination of site-specific glycosylation of SARS-CoV-2 viral spike protein. This is compounded by some conflicting results regarding glycan site occupancy and glycan structural characterization. These are probably due to differences in the expression systems, form of expressed spike glycoprotein, MS methodologies, and analysis software. In this review, we recap the glycosylation of spike protein and compare among various studies. Also, we describe the most recent advancements in glycosylation analysis in greater detail and we explain some misinterpretation of previously observed data in recent publications. Our study provides a comprehensive view of the spike protein glycosylation and highlights the importance of consistent glycosylation determination.
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Affiliation(s)
- Diana Campos
- Max‐Planck‐Institut fuer Herz‐ und LungenforschungBad NauheimGermany
| | - Michael Girgis
- Department of BioengineeringVolgenau School of Engineering and ComputingGeorge Mason UniversityFairfaxVirginiaUSA
| | - Miloslav Sanda
- Max‐Planck‐Institut fuer Herz‐ und LungenforschungBad NauheimGermany
- Clinical and Translational Glycoscience Research CenterGeorgetown UniversityWashingtonDCUSA
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15
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Azali MA, Mohamed S, Harun A, Hussain FA, Shamsuddin S, Johan MF. Application of Baculovirus Expression Vector system (BEV) for COVID-19 diagnostics and therapeutics: a review. J Genet Eng Biotechnol 2022; 20:98. [PMID: 35792966 PMCID: PMC9259773 DOI: 10.1186/s43141-022-00368-7] [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: 02/24/2022] [Accepted: 05/20/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND The baculovirus expression vector system has been developed for expressing a wide range of proteins, including enzymes, glycoproteins, recombinant viruses, and vaccines. The availability of the SARS-CoV-2 genome sequence has enabled the synthesis of SARS-CoV2 proteins in a baculovirus-insect cell platform for various applications. The most cloned SARS-CoV-2 protein is the spike protein, which plays a critical role in SARS-CoV-2 infection. It is available in its whole length or as subunits like S1 or the receptor-binding domain (RBD). Non-structural proteins (Nsps), another recombinant SARS-CoV-2 protein generated by the baculovirus expression vector system (BEV), are used in the identification of new medications or the repurposing of existing therapies for the treatment of COVID-19. Non-SARS-CoV-2 proteins generated by BEV for SARS-CoV-2 diagnosis or treatment include moloney murine leukemia virus reverse transcriptase (MMLVRT), angiotensin converting enzyme 2 (ACE2), therapeutic proteins, and recombinant antibodies. The recombinant proteins were modified to boost the yield or to stabilize the protein. CONCLUSION This review covers the wide application of the recombinant protein produced using the baculovirus expression technology for COVID-19 research. A lot of improvements have been made to produce functional proteins with high yields. However, there is still room for improvement and there are parts of this field of research that have not been investigated yet.
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Affiliation(s)
- Muhammad Azharuddin Azali
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.,School of Agriculture Science and Biotechnology, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, 22200, Besut, Terengganu, Malaysia
| | - Salmah Mohamed
- School of Agriculture Science and Biotechnology, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, 22200, Besut, Terengganu, Malaysia
| | - Azian Harun
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Faezahtul Arbaeyah Hussain
- Department of Pathology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Shaharum Shamsuddin
- School of Health Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Muhammad Farid Johan
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.
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16
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Asghar R, Rasheed M, ul Hassan J, Rafique M, Khan M, Deng Y. Advancements in Testing Strategies for COVID-19. BIOSENSORS 2022; 12:410. [PMID: 35735558 PMCID: PMC9220779 DOI: 10.3390/bios12060410] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 12/15/2022]
Abstract
The SARS-CoV-2 coronavirus, also known as the disease-causing agent for COVID-19, is a virulent pathogen that may infect people and certain animals. The global spread of COVID-19 and its emerging variation necessitates the development of rapid, reliable, simple, and low-cost diagnostic tools. Many methodologies and devices have been developed for the highly sensitive, selective, cost-effective, and rapid diagnosis of COVID-19. This review organizes the diagnosis platforms into four groups: imaging, molecular-based detection, serological testing, and biosensors. Each platform's principle, advancement, utilization, and challenges for monitoring SARS-CoV-2 are discussed in detail. In addition, an overview of the impact of variants on detection, commercially available kits, and readout signal analysis has been presented. This review will expand our understanding of developing advanced diagnostic approaches to evolve into susceptible, precise, and reproducible technologies to combat any future outbreak.
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Affiliation(s)
- Rabia Asghar
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China;
| | - Madiha Rasheed
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China;
| | - Jalees ul Hassan
- Department of Wildlife and Ecology, Faculty of Fisheries and Wildlife, University of Veterinary and Animal Sciences-UVAS, Lahore 54000, Pakistan;
| | - Mohsin Rafique
- Beijing Academy of Quantum Information Sciences, Beijing 100193, China;
| | - Mashooq Khan
- Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China;
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China;
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17
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Francesconi O, Donnici L, Fragai M, Pesce E, Bombaci M, Fasciani A, Manganaro L, Conti M, Grifantini R, De Francesco R, Nativi C, Roelens S. Synthetic carbohydrate-binding agents neutralize SARS-CoV-2 by inhibiting binding of the spike protein to ACE2. iScience 2022; 25:104239. [PMID: 35434540 PMCID: PMC8996466 DOI: 10.1016/j.isci.2022.104239] [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: 11/10/2021] [Revised: 03/21/2022] [Accepted: 04/06/2022] [Indexed: 11/26/2022] Open
Abstract
Developing strategies against the SARS-CoV-2 is currently a main research subject. SARS-CoV-2 infects host cells by binding to human ACE2 receptors. Both, virus and ACE2, are highly glycosylated, and exploiting glycans of the SARS-CoV-2 envelope as binding sites for ACE2 represents a virus strategy for attacking the human host. We report here that a family of mannose-binding synthetic carbohydrate-binding agents (CBAs) inhibits SARS-CoV-2 infection, showing broad neutralizing activity vs. several variants of the spike protein. Preliminary tests indicated that the investigated CBAs interact with the spike protein rather than with ACE2. For a lead compound (IDS060), which has been selected among others for its lack of cytotoxicity, evidence of binding to the RBD of the spike protein has been found by NMR experiments, while competitive binding assays in the presence of IDS060 showed inhibition of binding of RBD to hACE2, although neutralizing activity was also observed with variants showing reduced or depleted binding. Mannose-binding CBAs inhibit SARS-CoV-2 infection showing broad neutralizing activity CBAs interact with the spike protein rather than with ACE2 receptors The non-toxic CBA IDS060 binds to the spike RBD and inhibits binding of RBD to hACE2
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Affiliation(s)
- Oscar Francesconi
- Dipartimento di Chimica, DICUS, University of Florence, Florence, Italy
| | - Lorena Donnici
- Fondazione INGM - Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Marco Fragai
- Dipartimento di Chimica, DICUS, University of Florence, Florence, Italy.,CERM, University of Florence, Florence, Italy
| | - Elisa Pesce
- Fondazione INGM - Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Mauro Bombaci
- Fondazione INGM - Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Alessandra Fasciani
- Fondazione INGM - Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Lara Manganaro
- Fondazione INGM - Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy.,Dipartimento di Scienze Farmacologiche e Biomolecolari, University of Milan, Milan, Italy
| | - Matteo Conti
- Fondazione INGM - Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Renata Grifantini
- Fondazione INGM - Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Raffaele De Francesco
- Fondazione INGM - Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy.,Dipartimento di Scienze Farmacologiche e Biomolecolari, University of Milan, Milan, Italy
| | - Cristina Nativi
- Dipartimento di Chimica, DICUS, University of Florence, Florence, Italy
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18
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Van Ert HA, Bohan DW, Rogers K, Fili M, Rojas Chávez RA, Qing E, Han C, Dempewolf S, Hu G, Schwery N, Sevcik K, Ruggio N, Boyt D, Pentella MA, Gallagher T, Jackson JB, Merrill AE, Knudson CM, Brown GD, Maury W, Haim H. Limited Variation between SARS-CoV-2-Infected Individuals in Domain Specificity and Relative Potency of the Antibody Response against the Spike Glycoprotein. Microbiol Spectr 2022; 10:e0267621. [PMID: 35080430 PMCID: PMC8791189 DOI: 10.1128/spectrum.02676-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 12/28/2021] [Indexed: 11/25/2022] Open
Abstract
The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is arranged as a trimer on the virus surface, composed of three S1 and three S2 subunits. Infected and vaccinated individuals generate antibodies against spike, which can neutralize the virus. Most antibodies target the receptor-binding domain (RBD) and N-terminal domain (NTD) of S1; however, antibodies against other regions of spike have also been isolated. The interhost variability in domain specificity and relative neutralization efficacy of the antibodies is still poorly characterized. To this end, we tested serum and plasma samples collected from 85 coronavirus disease 2019 (COVID-19) convalescent subjects. Samples were analyzed using seven immunoassays that employ different domains, subunits, and oligomeric forms of spike to capture the antibodies. Samples were also tested for their neutralization of pseudovirus containing SARS-CoV-2 spike and of replication-competent SARS-CoV-2. While the total amount of anti-spike antibodies produced varied among convalescent subjects, we observed an unexpectedly fixed ratio of RBD- to NTD-targeting antibodies. The relative potency of the response (defined as the measured neutralization efficacy relative to the total level of spike-targeting antibodies) also exhibited limited variation between subjects and was not associated with the overall amount of antispike antibodies produced. These studies suggest that host-to-host variation in the polyclonal response elicited against SARS-CoV-2 spike in early pandemic subjects is primarily limited to the quantity of antibodies generated rather than their domain specificity or relative neutralization potency. IMPORTANCE Infection by SARS-CoV-2 elicits antibodies against various domains of the spike protein, including the RBD and NTD of subunit S1 and against subunit S2. The antibody responses of different infected individuals exhibit different efficacies to inactivate (neutralize) the virus. Here, we show that the observed variation in the neutralizing activity of the antibody responses in COVID-19 convalescent subjects is caused by differences in the amounts of antibodies rather than their recognition properties or the potency of their antiviral activity. These findings suggest that COVID-19 vaccine strategies that focus on enhancing the overall level of the antibodies will likely elicit a more uniformly efficacious protective response.
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Affiliation(s)
- Hanora A. Van Ert
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Dana W. Bohan
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Kai Rogers
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Mohammad Fili
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, Iowa, United States
| | - Roberth A. Rojas Chávez
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Enya Qing
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, United States
| | - Changze Han
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Spencer Dempewolf
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Guiping Hu
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, Iowa, United States
| | - Nathan Schwery
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Kristina Sevcik
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Natalie Ruggio
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Devlin Boyt
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Michael A. Pentella
- State Hygienic Laboratory, The University of Iowa, Iowa City, Iowa, United States
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, United States
| | - J. Brooks Jackson
- Department of Pathology, University of Iowa Hospitals & Clinics, Iowa City, Iowa, United States
| | - Anna E. Merrill
- Department of Pathology, University of Iowa Hospitals & Clinics, Iowa City, Iowa, United States
| | - C. Michael Knudson
- Department of Pathology, University of Iowa Hospitals & Clinics, Iowa City, Iowa, United States
| | - Grant D. Brown
- Department of Biostatistics, School of Public Health, The University of Iowa, Iowa City, Iowa, United States
| | - Wendy Maury
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
| | - Hillel Haim
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States
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19
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Known Cellular and Receptor Interactions of Animal and Human Coronaviruses: A Review. Viruses 2022; 14:v14020351. [PMID: 35215937 PMCID: PMC8878323 DOI: 10.3390/v14020351] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 12/12/2022] Open
Abstract
This article aims to review all currently known interactions between animal and human coronaviruses and their cellular receptors. Over the past 20 years, three novel coronaviruses have emerged that have caused severe disease in humans, including SARS-CoV-2 (severe acute respiratory syndrome virus 2); therefore, a deeper understanding of coronavirus host-cell interactions is essential. Receptor-binding is the first stage in coronavirus entry prior to replication and can be altered by minor changes within the spike protein-the coronavirus surface glycoprotein responsible for the recognition of cell-surface receptors. The recognition of receptors by coronaviruses is also a major determinant in infection, tropism, and pathogenesis and acts as a key target for host-immune surveillance and other potential intervention strategies. We aim to highlight the need for a continued in-depth understanding of this subject area following on from the SARS-CoV-2 pandemic, with the possibility for more zoonotic transmission events. We also acknowledge the need for more targeted research towards glycan-coronavirus interactions as zoonotic spillover events from animals to humans, following an alteration in glycan-binding capability, have been well-documented for other viruses such as Influenza A.
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