1
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Hattab D, Amer MFA, Al-Alami ZM, Bakhtiar A. SARS-CoV-2 journey: from alpha variant to omicron and its sub-variants. Infection 2024; 52:767-786. [PMID: 38554253 PMCID: PMC11143066 DOI: 10.1007/s15010-024-02223-y] [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: 12/27/2023] [Accepted: 02/22/2024] [Indexed: 04/01/2024]
Abstract
The COVID-19 pandemic has affected hundreds of millions of individuals and caused more than six million deaths. The prolonged pandemic duration and the continual inter-individual transmissibility have contributed to the emergence of a wide variety of SARS-CoV-2 variants. Genomic surveillance and phylogenetic studies have shown that substantial mutations in crucial supersites of spike glycoprotein modulate the binding affinity of the evolved SARS-COV-2 lineages to ACE2 receptors and modify the binding of spike protein with neutralizing antibodies. The immunological spike mutations have been associated with differential transmissibility, infectivity, and therapeutic efficacy of the vaccines and the immunological therapies among the new variants. This review highlights the diverse genetic mutations assimilated in various SARS-CoV-2 variants. The implications of the acquired mutations related to viral transmission, infectivity, and COVID-19 severity are discussed. This review also addresses the effectiveness of human neutralizing antibodies induced by SARS-CoV-2 infection or immunization and the therapeutic antibodies against the ascended variants.
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Affiliation(s)
- Dima Hattab
- School of Pharmacy, The University of Jordan, Queen Rania Street, Amman, Jordan
| | - Mumen F A Amer
- Faculty of Pharmacy, Applied Science Private University, Amman, Jordan
| | - Zina M Al-Alami
- Department of Basic Medical Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Athirah Bakhtiar
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.
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2
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Huang Y, Huang C, Chen J, Chen S, Li B, Li J, Jin Z, Zhang Q, Pan P, Du W, Liu L, Liu Z. Inhibition of SARS-CoV-2 replication by a ssDNA aptamer targeting the nucleocapsid protein. Microbiol Spectr 2024; 12:e0341023. [PMID: 38376366 PMCID: PMC10986557 DOI: 10.1128/spectrum.03410-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/01/2024] [Indexed: 02/21/2024] Open
Abstract
The nucleocapsid protein of SARS-CoV-2 plays significant roles in viral assembly, immune evasion, and viral stability. Due to its immunogenicity, high expression levels during COVID-19, and conservation across viral strains, it represents an attractive target for antiviral treatment. In this study, we identified and characterized a single-stranded DNA aptamer, N-Apt17, which effectively disrupts the liquid-liquid phase separation (LLPS) mediated by the N protein. To enhance the aptamer's stability, a circular bivalent form, cb-N-Apt17, was designed and evaluated. Our findings demonstrated that cb-N-Apt17 exhibited improved stability, enhanced binding affinity, and superior inhibition of N protein LLPS; thus, it has the potential inhibition ability on viral replication. These results provide valuable evidence supporting the potential of cb-N-Apt17 as a promising candidate for the development of antiviral therapies against COVID-19.IMPORTANCEVariants of SARS-CoV-2 pose a significant challenge to currently available COVID-19 vaccines and therapies due to the rapid epitope changes observed in the viral spike protein. However, the nucleocapsid (N) protein of SARS-CoV-2, a highly conserved structural protein, offers promising potential as a target for inhibiting viral replication. The N protein forms complexes with genomic RNA, interacts with other viral structural proteins during virion assembly, and plays a critical role in evading host innate immunity by impairing interferon production during viral infection. In this investigation, we discovered a single-stranded DNA aptamer, designated as N-Apt17, exhibiting remarkable affinity and specificity for the N protein. Notably, N-Apt17 disrupts the liquid-liquid phase separation (LLPS) of the N protein. To enhance the stability and molecular recognition capabilities of N-Apt17, we designed a circular bivalent DNA aptamer termed cb-N-Apt17. In both in vivo and in vitro experiments, cb-N-Apt17 exhibited increased stability, enhanced binding affinity, and superior LLPS disrupting ability. Thus, our study provides essential proof-of-principle evidence supporting the further development of cb-N-Apt17 as a therapeutic candidate for COVID-19.
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Affiliation(s)
- Yanping Huang
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Virology Key Laboratory of Shiyan City, Shiyan, China
| | - Congcong Huang
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Virology Key Laboratory of Shiyan City, Shiyan, China
| | - Junkai Chen
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Virology Key Laboratory of Shiyan City, Shiyan, China
| | - Siwei Chen
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Virology Key Laboratory of Shiyan City, Shiyan, China
| | - Bei Li
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Virology Key Laboratory of Shiyan City, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Jian Li
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Virology Key Laboratory of Shiyan City, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Zhixiong Jin
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Virology Key Laboratory of Shiyan City, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Qiwei Zhang
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Pan Pan
- The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Weixing Du
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Long Liu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Virology Key Laboratory of Shiyan City, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Zhixin Liu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Virology Key Laboratory of Shiyan City, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
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3
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Dhami LS, Dahal P, Thapa B, Gautam N, Pantha N, Adhikari R, Adhikari NP. Insights from in silico study of receptor energetics of SARS-CoV-2 variants. Phys Chem Chem Phys 2024; 26:8794-8806. [PMID: 38420855 DOI: 10.1039/d3cp04997c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The emergence of new variants of the novel coronavirus SARS-CoV-2 with increased infectivity, superior virulence, high transmissibility, and unmatched immune escape has demonstrated the adaptability and evolutionary fitness of the virus. The subject of relative order of the binding affinity of SARS-CoV-2 variants with the human ACE2 (hACE2) receptor is hotly debated and its resolution has implications for drug design and development. In this work, we have investigated the energetics of the binding of receptor binding domain (RBD) of SARS-CoV-2 variants of concern (VOCs): Beta (B.1.351), Delta (B.1.617.2), Omicron (B.1.1.529), variant of interest (VOI): Kappa (B.1.617.1), and Delta Plus (B.1.617.2.1) variant with the human ACE2 receptor by using the umbrella sampling (US) method. Our work indicates that Delta and Delta Plus variants have greater values of the US binding free energy than Wild-type (WT), whereas Beta, Kappa, and Omicron variants have lower values. Further analysis of hydrogen bonding, salt bridges, non-bonded interaction energy, and contact surface area at the RBD-hACE2 interface establish Delta as the variant with the highest binding affinity among these variants.
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Affiliation(s)
- Lokendra Singh Dhami
- Central Department of Physics, Tribhuvan University, Kirtipur, Kathmandu 44613, Nepal.
| | - Prabin Dahal
- Central Department of Physics, Tribhuvan University, Kirtipur, Kathmandu 44613, Nepal.
| | - Bidhya Thapa
- Central Department of Physics, Tribhuvan University, Kirtipur, Kathmandu 44613, Nepal.
- Padma Kanya Multiple Campus, Tribhuvan University, Bagbazar, Kathmandu 44613, Nepal
| | - Narayan Gautam
- Central Department of Physics, Tribhuvan University, Kirtipur, Kathmandu 44613, Nepal.
- Tri-chandra Multiple Campus, Tribhuvan University, Ghantaghar, Kathmandu 44613, Nepal
| | - Nurapati Pantha
- Central Department of Physics, Tribhuvan University, Kirtipur, Kathmandu 44613, Nepal.
| | - Rameshwar Adhikari
- Research Centre for Applied Science and Technology (RECAST), Tribhuvan University, Kirtipur, Kathmandu 44613, Nepal
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Gressett TE, Hossen ML, Talkington G, Volic M, Perez H, Tiwari PB, Chapagain P, Bix G. Molecular interactions between perlecan LG3 and the SARS-CoV-2 spike protein receptor binding domain. Protein Sci 2024; 33:e4843. [PMID: 37996967 PMCID: PMC10731540 DOI: 10.1002/pro.4843] [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: 06/18/2023] [Revised: 10/14/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused a global health crisis with significant clinical morbidity and mortality. While angiotensin-converting enzyme 2 (ACE2) is the primary receptor for viral entry, other cell surface and extracellular matrix proteins may also bind to the viral receptor binding domain (RBD) within the SARS-CoV-2 spike protein. Recent studies have implicated heparan sulfate proteoglycans, specifically perlecan LG3, in facilitating SARS-CoV-2 binding to ACE2. However, the role of perlecan LG3 in SARS-CoV-2 pathophysiology is not well understood. In this study, we investigated the binding interactions between the SARS-CoV-2 spike protein RBD and perlecan LG3 through molecular modeling simulations and surface plasmon resonance (SPR) experiments. Our results indicate stable binding between LG3 and SARS-CoV-2 spike protein RBD, which may potentially enhance RBD-ACE2 interactions. These findings shed light on the role of perlecan LG3 in SARS-CoV-2 infection and provide insight into SARS-CoV-2 pathophysiology and potential therapeutic strategy for COVID-19.
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Affiliation(s)
- Timothy E. Gressett
- Department of Neurosurgery, Clinical Neuroscience Research CenterTulane University School of MedicineNew OrleansLouisianaUSA
- Tulane Brain InstituteTulane UniversityNew OrleansLouisianaUSA
| | - Md Lokman Hossen
- Department of PhysicsFlorida International UniversityMiamiFloridaUSA
- Department of PhysicsUniversity of BarishalKornokathiBangladesh
| | - Grant Talkington
- Department of Neurosurgery, Clinical Neuroscience Research CenterTulane University School of MedicineNew OrleansLouisianaUSA
- Tulane Brain InstituteTulane UniversityNew OrleansLouisianaUSA
| | - Milla Volic
- Department of Neurosurgery, Clinical Neuroscience Research CenterTulane University School of MedicineNew OrleansLouisianaUSA
| | - Hugo Perez
- Department of PhysicsFlorida International UniversityMiamiFloridaUSA
| | | | - Prem Chapagain
- Department of PhysicsFlorida International UniversityMiamiFloridaUSA
- Biomolecular Sciences InstituteFlorida International UniversityMiamiFloridaUSA
| | - Gregory Bix
- Department of Neurosurgery, Clinical Neuroscience Research CenterTulane University School of MedicineNew OrleansLouisianaUSA
- Tulane Brain InstituteTulane UniversityNew OrleansLouisianaUSA
- Department of NeurologyTulane University School of MedicineNew OrleansLouisianaUSA
- Department of Microbiology and ImmunologyTulane University School of MedicineNew OrleansLouisianaUSA
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5
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Lipskij A, Arbeitman C, Rojas P, Ojeda-May P, Garcia ME. Dramatic Differences between the Structural Susceptibility of the S1 Pre- and S2 Postfusion States of the SARS-CoV-2 Spike Protein to External Electric Fields Revealed by Molecular Dynamics Simulations. Viruses 2023; 15:2405. [PMID: 38140646 PMCID: PMC10748067 DOI: 10.3390/v15122405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
In its prefusion state, the SARS-CoV-2 spike protein (similarly to other class I viral fusion proteins) is metastable, which is considered to be an important feature for optimizing or regulating its functions. After the binding process of its S1 subunit (S1) with ACE2, the spike protein (S) undergoes a dramatic conformational change where S1 splits from the S2 subunit, which then penetrates the membrane of the host cell, promoting the fusion of the viral and cell membranes. This results in the infection of the host cell. In a previous work, we showed-using large-scale molecular dynamics simulations-that the application of external electric fields (EFs) induces drastic changes and damage in the receptor-binding domain (RBD) of the wild-type spike protein, as well of the Alpha, Beta, and Gamma variants, leaving a structure which cannot be recognized anymore by ACE2. In this work, we first extend the study to the Delta and Omicron variants and confirm the high sensitivity and extreme vulnerability of the RBD of the prefusion state of S to moderate EF (as weak as 104 V/m), but, more importantly, we also show that, in contrast, the S2 subunit of the postfusion state of the spike protein does not suffer structural damage even if electric field intensities four orders of magnitude higher are applied. These results provide a solid scientific basis to confirm the connection between the prefusion-state metastability of the SARS-CoV-2 spike protein and its susceptibility to be damaged by EF. After the virus docks to the ACE2 receptor, the stable and robust postfusion conformation develops, which exhibits a similar resistance to EF (damage threshold higher than 108 V/m) like most globular proteins.
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Affiliation(s)
- Alexander Lipskij
- Theoretical Physics and Center of Interdisciplinary Nanostructure Science and Technology, FB10, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany; (A.L.); (C.A.); (P.R.)
| | - Claudia Arbeitman
- Theoretical Physics and Center of Interdisciplinary Nanostructure Science and Technology, FB10, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany; (A.L.); (C.A.); (P.R.)
- CONICET Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, Buenos Aires C1425FQB, Argentina
- GIBIO-Universidad Tecnológica Nacional-Facultad Regional Buenos Aires, Medrano 951, Buenos Aires C1179AAQ, Argentina
| | - Pablo Rojas
- Theoretical Physics and Center of Interdisciplinary Nanostructure Science and Technology, FB10, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany; (A.L.); (C.A.); (P.R.)
| | - Pedro Ojeda-May
- High Performance Computing Center North (HPC2N), Umeå University, S-90187 Umeå, Sweden;
| | - Martin E. Garcia
- Theoretical Physics and Center of Interdisciplinary Nanostructure Science and Technology, FB10, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany; (A.L.); (C.A.); (P.R.)
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6
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de Souza AS, de Souza RF, Guzzo CR. Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1). J Comput Aided Mol Des 2023; 37:585-606. [PMID: 37792106 DOI: 10.1007/s10822-023-00534-0] [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: 09/11/2023] [Indexed: 10/05/2023]
Abstract
Herein, we conducted simulations of trimeric Spike from several SARS-CoV-2 variants of concern (Delta and Omicron sub-variants BA.2, BA.5, and BQ.1) and investigated the mechanisms by which specific mutations confer resistance to neutralizing antibodies. We observed that the mutations primarily affect the cooperation between protein domains within and between protomers. The substitutions K417N and L452R expand hydrogen bonding interactions, reducing their interaction with neutralizing antibodies. By interacting with nearby residues, the K444T and N460K mutations in the SpikeBQ.1 variant potentially reduces solvent exposure, thereby promoting resistance to antibodies. We also examined the impact of D614G, P681R, and P681H substitutions on Spike protein structure that may be related to infectivity. The D614G substitution influences communication between a glycine residue and neighboring domains, affecting the transition between up- and -down RBD states. The P681R mutation, found in the Delta variant, enhances correlations between protein subunits, while the P681H mutation in Omicron sub-variants weakens long-range interactions that may be associated with reduced fusogenicity. Using a multiple linear regression model, we established a connection between inter-protomer communication and loss of sensitivity to neutralizing antibodies. Our findings underscore the importance of structural communication between protein domains and provide insights into potential mechanisms of immune evasion by SARS-CoV-2. Overall, this study deepens our understanding of how specific mutations impact SARS-CoV-2 infectivity and shed light on how the virus evades the immune system.
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Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil.
| | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil.
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7
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Coelho FF, da Silva MA, Lopes TB, Polatto JM, de Castro NS, Andrade LAF, Lourenço KL, Sato HI, de Carvalho AF, Coelho HP, Bagno FF, Luz D, Viala VL, Cattony PQ, Melo BDS, Moro AM, Quintilio W, Barbosa AP, Bomfim CG, Soares CP, Guzzo CR, Fonseca FG, Durigon EL, Gazzinelli RT, Ribeiro Teixeira SM, Piazza RMF, Fernandes AP. SARS-CoV-2 Rapid Antigen Test Based on a New Anti-Nucleocapsid Protein Monoclonal Antibody: Development and Real-Time Validation. Microorganisms 2023; 11:2422. [PMID: 37894080 PMCID: PMC10608853 DOI: 10.3390/microorganisms11102422] [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: 07/12/2023] [Revised: 08/27/2023] [Accepted: 09/01/2023] [Indexed: 10/29/2023] Open
Abstract
SARS-CoV-2 diagnostic tests have become an important tool for pandemic control. Among the alternatives for COVID-19 diagnosis, antigen rapid diagnostic tests (Ag-RDT) are very convenient and widely used. However, as SARS-CoV-2 variants may continuously emerge, the replacement of tests and reagents may be required to maintain the sensitivity of Ag-RDTs. Here, we describe the development and validation of an Ag-RDT during an outbreak of the Omicron variant, including the characterization of a new monoclonal antibody (anti-DTC-N 1B3 mAb) that recognizes the Nucleocapsid protein (N). The anti-DTC-N 1B3 mAb recognized the sequence TFPPTEPKKDKKK located at the C-terminus of the N protein of main SARS-CoV-2 variants of concern. Accordingly, the Ag-RDT prototypes using the anti-DTC-N 1B3 mAB detected all the SARS-CoV-2 variants-Wuhan, Alpha, Gamma, Delta, P2 and Omicron. The performance of the best prototype (sensitivity of 95.2% for samples with Ct ≤ 25; specificity of 98.3% and overall accuracy of 85.0%) met the WHO recommendations. Moreover, results from a patients' follow-up study indicated that, if performed within the first three days after onset of symptoms, the Ag-RDT displayed 100% sensitivity. Thus, the new mAb and the Ag-RDT developed herein may constitute alternative tools for COVID-19 point-of-care diagnosis and epidemiological surveillance.
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Affiliation(s)
- Fabiana Fioravante Coelho
- Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil;
- Hospital da Polícia Militar de Minas Gerais, Polícia Militar de Minas Gerais, Belo Horizonte 30110-013, Brazil
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte 31310-260, Brazil; (T.B.L.); (N.S.d.C.); (L.A.F.A.); (K.L.L.); (H.I.S.); (A.F.d.C.); (H.P.C.); (F.F.B.); (F.G.F.); (R.T.G.); (S.M.R.T.)
| | - Miriam Aparecida da Silva
- Instituto Butantan, São Paulo 05503-900, Brazil; (M.A.d.S.); (J.M.P.); (D.L.); (V.L.V.); (P.Q.C.); (B.d.S.M.); (A.M.M.); (W.Q.); (A.P.B.); (R.M.F.P.)
| | - Thiciany Blener Lopes
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte 31310-260, Brazil; (T.B.L.); (N.S.d.C.); (L.A.F.A.); (K.L.L.); (H.I.S.); (A.F.d.C.); (H.P.C.); (F.F.B.); (F.G.F.); (R.T.G.); (S.M.R.T.)
| | - Juliana Moutinho Polatto
- Instituto Butantan, São Paulo 05503-900, Brazil; (M.A.d.S.); (J.M.P.); (D.L.); (V.L.V.); (P.Q.C.); (B.d.S.M.); (A.M.M.); (W.Q.); (A.P.B.); (R.M.F.P.)
| | - Natália Salazar de Castro
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte 31310-260, Brazil; (T.B.L.); (N.S.d.C.); (L.A.F.A.); (K.L.L.); (H.I.S.); (A.F.d.C.); (H.P.C.); (F.F.B.); (F.G.F.); (R.T.G.); (S.M.R.T.)
| | - Luis Adan Flores Andrade
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte 31310-260, Brazil; (T.B.L.); (N.S.d.C.); (L.A.F.A.); (K.L.L.); (H.I.S.); (A.F.d.C.); (H.P.C.); (F.F.B.); (F.G.F.); (R.T.G.); (S.M.R.T.)
| | - Karine Lima Lourenço
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte 31310-260, Brazil; (T.B.L.); (N.S.d.C.); (L.A.F.A.); (K.L.L.); (H.I.S.); (A.F.d.C.); (H.P.C.); (F.F.B.); (F.G.F.); (R.T.G.); (S.M.R.T.)
| | - Hugo Itaru Sato
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte 31310-260, Brazil; (T.B.L.); (N.S.d.C.); (L.A.F.A.); (K.L.L.); (H.I.S.); (A.F.d.C.); (H.P.C.); (F.F.B.); (F.G.F.); (R.T.G.); (S.M.R.T.)
| | - Alex Fiorini de Carvalho
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte 31310-260, Brazil; (T.B.L.); (N.S.d.C.); (L.A.F.A.); (K.L.L.); (H.I.S.); (A.F.d.C.); (H.P.C.); (F.F.B.); (F.G.F.); (R.T.G.); (S.M.R.T.)
| | - Helena Perez Coelho
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte 31310-260, Brazil; (T.B.L.); (N.S.d.C.); (L.A.F.A.); (K.L.L.); (H.I.S.); (A.F.d.C.); (H.P.C.); (F.F.B.); (F.G.F.); (R.T.G.); (S.M.R.T.)
| | - Flávia Fonseca Bagno
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte 31310-260, Brazil; (T.B.L.); (N.S.d.C.); (L.A.F.A.); (K.L.L.); (H.I.S.); (A.F.d.C.); (H.P.C.); (F.F.B.); (F.G.F.); (R.T.G.); (S.M.R.T.)
| | - Daniela Luz
- Instituto Butantan, São Paulo 05503-900, Brazil; (M.A.d.S.); (J.M.P.); (D.L.); (V.L.V.); (P.Q.C.); (B.d.S.M.); (A.M.M.); (W.Q.); (A.P.B.); (R.M.F.P.)
| | - Vincent Louis Viala
- Instituto Butantan, São Paulo 05503-900, Brazil; (M.A.d.S.); (J.M.P.); (D.L.); (V.L.V.); (P.Q.C.); (B.d.S.M.); (A.M.M.); (W.Q.); (A.P.B.); (R.M.F.P.)
| | - Pedro Queiroz Cattony
- Instituto Butantan, São Paulo 05503-900, Brazil; (M.A.d.S.); (J.M.P.); (D.L.); (V.L.V.); (P.Q.C.); (B.d.S.M.); (A.M.M.); (W.Q.); (A.P.B.); (R.M.F.P.)
| | - Bruna de Sousa Melo
- Instituto Butantan, São Paulo 05503-900, Brazil; (M.A.d.S.); (J.M.P.); (D.L.); (V.L.V.); (P.Q.C.); (B.d.S.M.); (A.M.M.); (W.Q.); (A.P.B.); (R.M.F.P.)
| | - Ana Maria Moro
- Instituto Butantan, São Paulo 05503-900, Brazil; (M.A.d.S.); (J.M.P.); (D.L.); (V.L.V.); (P.Q.C.); (B.d.S.M.); (A.M.M.); (W.Q.); (A.P.B.); (R.M.F.P.)
| | - Wagner Quintilio
- Instituto Butantan, São Paulo 05503-900, Brazil; (M.A.d.S.); (J.M.P.); (D.L.); (V.L.V.); (P.Q.C.); (B.d.S.M.); (A.M.M.); (W.Q.); (A.P.B.); (R.M.F.P.)
| | - Ana Paula Barbosa
- Instituto Butantan, São Paulo 05503-900, Brazil; (M.A.d.S.); (J.M.P.); (D.L.); (V.L.V.); (P.Q.C.); (B.d.S.M.); (A.M.M.); (W.Q.); (A.P.B.); (R.M.F.P.)
| | - Camila Gasque Bomfim
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-900, Brazil; (C.G.B.); (C.P.S.); (C.R.G.); (E.L.D.)
| | - Camila Pereira Soares
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-900, Brazil; (C.G.B.); (C.P.S.); (C.R.G.); (E.L.D.)
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-900, Brazil; (C.G.B.); (C.P.S.); (C.R.G.); (E.L.D.)
| | - Flavio Guimarães Fonseca
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte 31310-260, Brazil; (T.B.L.); (N.S.d.C.); (L.A.F.A.); (K.L.L.); (H.I.S.); (A.F.d.C.); (H.P.C.); (F.F.B.); (F.G.F.); (R.T.G.); (S.M.R.T.)
| | - Edison Luiz Durigon
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-900, Brazil; (C.G.B.); (C.P.S.); (C.R.G.); (E.L.D.)
| | - Ricardo Tostes Gazzinelli
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte 31310-260, Brazil; (T.B.L.); (N.S.d.C.); (L.A.F.A.); (K.L.L.); (H.I.S.); (A.F.d.C.); (H.P.C.); (F.F.B.); (F.G.F.); (R.T.G.); (S.M.R.T.)
| | - Santuza M. Ribeiro Teixeira
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte 31310-260, Brazil; (T.B.L.); (N.S.d.C.); (L.A.F.A.); (K.L.L.); (H.I.S.); (A.F.d.C.); (H.P.C.); (F.F.B.); (F.G.F.); (R.T.G.); (S.M.R.T.)
| | - Roxane Maria Fontes Piazza
- Instituto Butantan, São Paulo 05503-900, Brazil; (M.A.d.S.); (J.M.P.); (D.L.); (V.L.V.); (P.Q.C.); (B.d.S.M.); (A.M.M.); (W.Q.); (A.P.B.); (R.M.F.P.)
| | - Ana Paula Fernandes
- Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil;
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte 31310-260, Brazil; (T.B.L.); (N.S.d.C.); (L.A.F.A.); (K.L.L.); (H.I.S.); (A.F.d.C.); (H.P.C.); (F.F.B.); (F.G.F.); (R.T.G.); (S.M.R.T.)
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8
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Sharma T, Gerstman B, Chapagain P. Distinctive Features of the XBB.1.5 and XBB.1.16 Spike Protein Receptor-Binding Domains and Their Roles in Conformational Changes and Angiotensin-Converting Enzyme 2 Binding. Int J Mol Sci 2023; 24:12586. [PMID: 37628766 PMCID: PMC10454900 DOI: 10.3390/ijms241612586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
The emergence and the high transmissibility of the XBB.1.5 and XBB.1.16 subvariants of the SARS-CoV-2 omicron has reignited concerns over the potential impact on vaccine efficacy for these and future variants. We investigated the roles of the XBB.1.5 and XBB.1.16 mutations on the structure of the spike protein's receptor-binding domain (RBD) and its interactions with the host cell receptor ACE2. To bind to ACE2, the RBD must transition from the closed-form to the open-form configuration. We found that the XBB variants have less stable closed-form structures that may make the transition to the open-form easier. We found that the mutations enhance the RBD-ACE2 interactions in XBB.1.16 compared to XBB.1.5. We observed significant structural changes in the loop and motif regions of the RBD, altering well-known antibody-binding sites and potentially rendering primary RBD-specific antibodies ineffective. Our findings elucidate how subtle structural changes and interactions contribute to the subvariants' fitness over their predecessors.
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Affiliation(s)
- Tej Sharma
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Bernard Gerstman
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
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9
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Sun L, Wang L, Zhang C, Xiao Y, Zhang L, Zhao Z, Ren L, Peng J. Rapid Detection of Predominant SARS-CoV-2 Variants Using Multiplex High-Resolution Melting Analysis. Microbiol Spectr 2023; 11:e0005523. [PMID: 37191515 PMCID: PMC10269585 DOI: 10.1128/spectrum.00055-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
Coronavirus disease 2019, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses a considerable threat to global public health. This study developed and evaluated a rapid, low-cost, expandable, and sequencing-free high-resolution melting (HRM) assay for the direct detection of SARS-CoV-2 variants. A panel of 64 common bacterial and viral pathogens that can cause respiratory tract infections was employed to evaluate our method's specificity. Serial dilutions of viral isolates determined the sensitivity of the method. Finally, the assay's clinical performance was assessed using 324 clinical samples with potential SARS-CoV-2 infection. Multiplex HRM analysis accurately identified SARS-CoV-2 (as confirmed with parallel reverse transcription-quantitative PCR [qRT-PCR] tests), differentiating between mutations at each marker site within approximately 2 h. For each target, the limit of detection (LOD) was lower than 10 copies/reaction (the LOD of N, G142D, R158G, Y505H, V213G, G446S, S413R, F486V, and S704L was 7.38, 9.72, 9.96, 9.96, 9.50, 7.80, 9.33, 8.25, and 8.25 copies/reaction, respectively). No cross-reactivity occurred with organisms of the specificity testing panel. In terms of variant detection, our results had a 97.9% (47/48) rate of agreement with standard Sanger sequencing. The multiplex HRM assay therefore offers a rapid and simple procedure for detecting SARS-CoV-2 variants. IMPORTANCE In the face of the current severe situation of increasing SARS-CoV-2 variants, we developed an upgraded multiplex HRM method for the predominant SARS-CoV-2 variants based on our original research. This method not only could identify the variants but also could be utilized in subsequent detection of novel variants since the assay has great performance in terms of flexibility. In summary, the upgraded multiplex HRM assay is a rapid, reliable, and economical detection method, which could better screen prevalent virus strains, monitor the epidemic situation, and help to develop measures for the prevention and control of SARS-CoV-2.
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Affiliation(s)
- Liying Sun
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liqin Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chi Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yan Xiao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lulu Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ziyuan Zhao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lili Ren
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Junping Peng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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10
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Ye J, Shao X, Yang Y, Zhu F. Predicting the negative conversion time of nonsevere COVID-19 patients using machine learning methods. J Med Virol 2023; 95:e28747. [PMID: 37185847 DOI: 10.1002/jmv.28747] [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: 01/19/2023] [Revised: 03/10/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023]
Abstract
Based on the patient's clinical characteristics and laboratory indicators, different machine-learning methods were used to develop models for predicting the negative conversion time of nonsevere coronavirus disease 2019 (COVID-19) patients. A retrospective analysis was performed on 376 nonsevere COVID-19 patients admitted to Wuxi Fifth People's Hospital from May 2, 2022, to May 14, 2022. The patients were divided into training set (n = 309) and test set (n = 67). The clinical features and laboratory parameters of the patients were collected. In the training set, the least absolute shrinkage and selection operator (LASSO) was used to select predictive features and train six machine learning models: multiple linear regression (MLR), K-Nearest Neighbors Regression (KNNR), random forest regression (RFR), support vector machine regression (SVR), XGBoost regression (XGBR), and multilayer perceptron regression (MLPR). Seven best predictive features selected by LASSO included: age, gender, vaccination status, IgG, lymphocyte ratio, monocyte ratio, and lymphocyte count. The predictive performance of the models in the test set was MLPR > SVR > MLR > KNNR > XGBR > RFR, and MLPR had the strongest generalization performance, which is significantly better than SVR and MLR. In the MLPR model, vaccination status, IgG, lymphocyte count, and lymphocyte ratio were protective factors for negative conversion time; male gender, age, and monocyte ratio were risk factors. The top three features with the highest weights were vaccination status, gender, and IgG. Machine learning methods (especially MLPR) can effectively predict the negative conversion time of non-severe COVID-19 patients. It can help to rationally allocate limited medical resources and prevent disease transmission, especially during the Omicron pandemic.
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Affiliation(s)
- Jiru Ye
- Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Xiaonan Shao
- Department of Nuclear Medicine, The Third Affiliated Hospital of Soochow University, Institute of Clinical Translation of Nuclear Medicine and Molecular Imaging of Soochow University, Changzhou Clinical Medical Center, Changzhou, China
| | - Yong Yang
- Department of Pediatrics, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Feng Zhu
- Department of Respiratory and Critical Care Medicine, Affiliated Wuxi Fifth Hospital of Jiangnan University, Wuxi Fifth People's Hospital, Wuxi, China
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11
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Harne R, Williams B, Abdelaal HFM, Baldwin SL, Coler RN. SARS-CoV-2 infection and immune responses. AIMS Microbiol 2023; 9:245-276. [PMID: 37091818 PMCID: PMC10113164 DOI: 10.3934/microbiol.2023015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 04/03/2023] Open
Abstract
The recent pandemic caused by the SARS-CoV-2 virus continues to be an enormous global challenge faced by the healthcare sector. Availability of new vaccines and drugs targeting SARS-CoV-2 and sequelae of COVID-19 has given the world hope in ending the pandemic. However, the emergence of mutations in the SARS-CoV-2 viral genome every couple of months in different parts of world is a persistent danger to public health. Currently there is no single treatment to eradicate the risk of COVID-19. The widespread transmission of SARS-CoV-2 due to the Omicron variant necessitates continued work on the development and implementation of effective vaccines. Moreover, there is evidence that mutations in the receptor domain of the SARS-CoV-2 spike glycoprotein led to the decrease in current vaccine efficacy by escaping antibody recognition. Therefore, it is essential to actively identify the mechanisms by which SARS-CoV-2 evades the host immune system, study the long-lasting effects of COVID-19 and develop therapeutics targeting SARS-CoV-2 infections in humans and preclinical models. In this review, we describe the pathogenic mechanisms of SARS-CoV-2 infection as well as the innate and adaptive host immune responses to infection. We address the ongoing need to develop effective vaccines that provide protection against different variants of SARS-CoV-2, as well as validated endpoint assays to evaluate the immunogenicity of vaccines in the pipeline, medications, anti-viral drug therapies and public health measures, that will be required to successfully end the COVID-19 pandemic.
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Affiliation(s)
- Rakhi Harne
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
| | - Brittany Williams
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Hazem F. M. Abdelaal
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
| | - Susan L. Baldwin
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
| | - Rhea N. Coler
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
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12
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Cheng Y, Zheng D, Zhang D, Guo D, Wang Y, Liu W, Liang L, Hu J, Luo T. Molecular recognition of SARS-CoV-2 spike protein with three essential partners: exploring possible immune escape mechanisms of viral mutants. J Mol Model 2023; 29:109. [PMID: 36964244 PMCID: PMC10038388 DOI: 10.1007/s00894-023-05509-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/10/2023] [Indexed: 03/26/2023]
Abstract
OBJECTIVE The COVID-19 epidemic is raging around the world, with the emergence of viral mutant strains such as Delta and Omicron, posing severe challenges to people's health and quality of life. A full understanding life cycle of the virus in host cells helps to reveal inactivation mechanism of antibody and provide inspiration for the development of a new-generation vaccines. METHODS In this work, molecular recognitions and conformational changes of SARS-CoV-2 spike protein mutants (i.e., Delta, Mu, and Omicron) and three essential partners (i.e., membrane receptor hACE2, protease TMPRSS2, and antibody C121) both were compared and analyzed using molecular simulations. RESULTS Water basin and binding free energy calculations both show that the three mutants possess higher affinity for hACE2 than WT, exhibiting stronger virus transmission. The descending order of cleavage ability by TMPRSS2 is Mu, Delta, Omicron, and WT, which is related to the new S1/S2 cutting site induced by transposition effect. The inefficient utilization of TMPRSS2 by Omicron is consistent with its primary entry into cells via the endosomal pathway. In addition, RBD-directed antibody C121 showed obvious resistance to Omicron, which may have originated from high fluctuation of approaching angles, high flexibility of I472-F490 loop, and reduced binding ability. CONCLUSIONS According to the overall characteristics of the three mutants, high infectivity, high immune escape, and low virulence may be the future evolutionary selection of SARS-CoV-2. In a word, this work not only proposes the possible resistance mechanism of SARS-CoV-2 mutants, but also provides theoretical guidance for the subsequent drug design against COVID-19 based on S protein structure.
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Affiliation(s)
- Yan Cheng
- Breast Disease Center, West China Hospital, Sichuan University, Cancer CenterChengdu, 610000, China
| | - Dan Zheng
- Breast Disease Center, West China Hospital, Sichuan University, Cancer CenterChengdu, 610000, China
| | - Derong Zhang
- School of Marxism, Chengdu Vocational & Technical College of Industry, Chengdu, China
| | - Du Guo
- Breast Disease Center, West China Hospital, Sichuan University, Cancer CenterChengdu, 610000, China
| | - Yueteng Wang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Wei Liu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Li Liang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Ting Luo
- Breast Disease Center, West China Hospital, Sichuan University, Cancer CenterChengdu, 610000, China.
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13
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Philipp M, Müller L, Andrée M, Hussnaetter KP, Schaal H, Feldbrügge M, Schipper K. Efficient virus detection utilizing chitin-immobilized nanobodies synthesized in Ustilago maydis. J Biotechnol 2023; 366:72-84. [PMID: 36948402 PMCID: PMC10028217 DOI: 10.1016/j.jbiotec.2023.03.005] [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: 12/12/2022] [Revised: 02/08/2023] [Accepted: 03/16/2023] [Indexed: 03/24/2023]
Abstract
The COVID-19 pandemic has greatly impacted the global economy and health care systems, illustrating the urgent need for timely and inexpensive responses to pandemic threats in the form of vaccines and antigen tests. Currently, antigen testing is mostly conducted by qualitative flow chromatography or via quantitative ELISA-type assays. The latter mostly utilize materials like protein-adhesive polymers and gold or latex particles. Here we present an alternative ELISA approach using inexpensive, biogenic materials and permitting quick detection based on components produced in the microbial model Ustilago maydis. In this fungus, heterologous proteins like biopharmaceuticals can be exported by fusion to unconventionally secreted chitinase Cts1. As a unique feature, the carrier chitinase binds to chitin allowing its additional use as a purification or immobilization tag. Recent work has demonstrated that nanobodies are suitable target proteins. These proteins represent a very versatile alternative antibody format and can quickly be adapted to detect novel antigens by camelidae immunization or synthetic libraries. In this study, we exemplarily produced different mono- and bivalent SARS-CoV-2 nanobodies directed against the spike protein receptor binding domain (RBD) as Cts1 fusions and screened their antigen binding affinity in vitro and in vivo. Functional nanobody-Cts1 fusions were immobilized on chitin forming an RBD tethering surface. This provides a solid base for future development of inexpensive antigen tests utilizing unconventionally secreted nanobodies as antigen trap and a matching ubiquitous and biogenic surface for immobilization.
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Affiliation(s)
- Magnus Philipp
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Lisa Müller
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Marcel Andrée
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Kai P Hussnaetter
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Michael Feldbrügge
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Kerstin Schipper
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany.
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14
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Bhattacharya M, Chatterjee S, Sharma AR, Lee SS, Chakraborty C. Delta variant (B.1.617.2) of SARS-CoV-2: current understanding of infection, transmission, immune escape, and mutational landscape. Folia Microbiol (Praha) 2023; 68:17-28. [PMID: 35962276 PMCID: PMC9374302 DOI: 10.1007/s12223-022-01001-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/07/2022] [Indexed: 12/01/2022]
Abstract
The Delta variant is one of the alarming variants of the SARS-CoV-2 virus that have been immensely detrimental and a significant cause of the prolonged pandemic (B.1.617.2). During the SARS-CoV-2 pandemic from December 2020 to October 2021, the Delta variant showed global dominance, and afterwards, the Omicron variant showed global dominance. Delta shows high infectivity rate which accounted for nearly 70% of the cases after December 2020. This review discusses the additional attributes that make the Delta variant so infectious and transmissible. The study also focuses on the significant mutations, namely the L452R and T478K present on the receptor-binding domain of spike (S)-glycoprotein, which confers specific alterations to the Delta variant. Considerably, we have also highlighted other notable factors such as the immune escape, infectivity and re-infectivity, vaccine escape, Ro number, S-glycoprotein stability, cleavage pattern, and its binding affinity with the host cell receptor protein. We have also emphasized clinical manifestations, symptomatology, morbidity, and mortality for the Delta variant compared with other significant SARS-CoV-2 variants. This review will help the researchers to get an elucidative view of the Delta variant to adopt some practical strategies to minimize the escalating spread of the SARS-CoV-2 Delta variant.
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Affiliation(s)
- Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore-756020, Odisha, India
| | - Srijan Chatterjee
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, 700126, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252, Gangwon-do, Republic of Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252, Gangwon-do, Republic of Korea
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, 700126, India.
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15
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Majed SO, Mustafa SA, Jalal PJ, Fatah MH, Miasko M, Jawhar Z, Karim AY. SARS-CoV-2 Omicron Variant Genomic and Phylogenetic Analysis in Iraqi Kurdistan Region. Genes (Basel) 2023; 14:173. [PMID: 36672914 PMCID: PMC9859166 DOI: 10.3390/genes14010173] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/31/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
Omicron variants have been classified as Variants of Concern (VOC) by the World Health Organization (WHO) ever since they first emerged as a result of a significant mutation in this variant, which showed to have an impact on transmissibility and virulence of the virus, as evidenced by the ongoing modifications in the SARS-CoV-2 virus. As a global pandemic, the Omicron variant also spread among the Kurdish population. This study aimed to analyze different strains from different cities of the Kurdistan region of Iraq to show the risk of infection and the impact of the various mutations on immune responses and vaccination. A total of 175 nasopharyngeal/oropharyngeal specimens were collected at West Erbil Emergency Hospital and confirmed for SARS-CoV-2 infection by RT-PCR. The genomes of the samples were sequenced using the Illumina COVID-Seq Method. The genome analysis was established based on previously published data in the GISAID database and compared to previously detected mutations in the Omicron variants, and that they belong to the BA.1 lineage and include most variations determined in other studies related to transmissibility, high infectivity and immune escape. Most of the mutations were found in the RBD (receptor binding domain), the region related to the escape from humoral immunity. Remarkably, these point mutations (G339D, S371L, S373P, S375F, T547K, D614G, H655Y, N679K and N969K) were also determined in this study, which were unique, and their impact should be addressed more. Overall, the Omicron variants were more contagious than other variants. However, the mortality rate was low, and most infectious cases were asymptomatic. The next step should address the potential of Omicron variants to develop the next-generation COVID-19 vaccine.
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Affiliation(s)
- Sevan Omer Majed
- Biology Department, College of Education, Salahaddin University-Erbil, Erbil 44001, Kurdistan Region, Iraq
| | - Suhad Asad Mustafa
- General Directorate of Scientific Research Center, Salahaddin University-Erbil, Erbil 44001, Kurdistan Region, Iraq
| | - Paywast Jamal Jalal
- Biology Department, College of Science, University of Sulaimani, Sulaymaniyah 46001, Kurdistan Region, Iraq
| | - Mohammed Hassan Fatah
- Medical Lab., Technology Department, Kalar Technical College, Sulaimani Polytechnic University, Kalar 46021, Kurdistan Region, Iraq
| | - Monika Miasko
- Medical Analysis Department, Faculty of Applied Science, Tishk International University, Erbil 44001, Kurdistan Region, Iraq
| | - Zanko Jawhar
- Medical Laboratory Science, College of Health Sciences, Lebanese French University, Erbil 44001, Kurdistan Region, Iraq
| | - Abdulkarim Yasin Karim
- Department of Biology, College of Science, Salahaddin University-Erbil, Erbil 44001, Kurdistan Region, Iraq
- Department of Medical Microbiology, College of Science, Cihan University, Erbil 44001,Kurdistan Region, Iraq
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16
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Puenpa J, Rattanakomol P, Saengdao N, Chansaenroj J, Yorsaeng R, Suwannakarn K, Thanasitthichai S, Vongpunsawad S, Poovorawan Y. Molecular characterisation and tracking of severe acute respiratory syndrome coronavirus 2 in Thailand, 2020-2022. Arch Virol 2023; 168:26. [PMID: 36593392 PMCID: PMC9807426 DOI: 10.1007/s00705-022-05666-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/30/2022] [Indexed: 01/04/2023]
Abstract
The global COVID-19 pandemic, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first detected in China in December 2019. To date, there have been approximately 3.4 million reported cases of COVID-19 and over 24,000 deaths in Thailand. In this study, we investigated the molecular characteristics and evolution of SARS-CoV-2 in Thailand from 2020 to 2022. Two hundred sixty-eight SARS-CoV-2 isolates, collected mostly in Bangkok from COVID-19 patients, were characterised by partial genome sequencing. Moreover, the viruses in 5,627 positive SARS-CoV-2 samples were identified as viral variants - B.1.1.7 (Alpha), B.1.617.2 (Delta), B.1.1.529 (Omicron/BA.1), or B.1.1.529 (Omicron/BA.2) - by multiplex real-time reverse transcription polymerase chain reaction (RT-PCR) assays. The results revealed that B.1.36.16 caused the predominant outbreak in the second wave (December 2020-January 2021), B.1.1.7 (Alpha) in the third wave (April-June 2021), B.1.617.2 (Delta) in the fourth wave (July-December 2021), and B.1.1.529 (Omicron) in the fifth wave (January-March 2022). The evolutionary rate of the viral genome was 2.60 × 10-3 (95% highest posterior density [HPD], 1.72 × 10-3 to 3.62 × 10-3) nucleotide substitutions per site per year. Continued molecular surveillance of SARS-CoV-2 is crucial for monitoring emerging variants with the potential to cause new COVID-19 outbreaks.
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Affiliation(s)
- Jiratchaya Puenpa
- grid.7922.e0000 0001 0244 7875Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Patthaya Rattanakomol
- grid.7922.e0000 0001 0244 7875Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nutsada Saengdao
- grid.7922.e0000 0001 0244 7875Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand ,grid.416009.aDepartment of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jira Chansaenroj
- grid.7922.e0000 0001 0244 7875Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ritthideach Yorsaeng
- grid.7922.e0000 0001 0244 7875Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kamol Suwannakarn
- grid.416009.aDepartment of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Somchai Thanasitthichai
- grid.415836.d0000 0004 0576 2573Institute of Medical Research and Technology Assessment, Ministry of Public Health, Bangkok, Thailand
| | - Sompong Vongpunsawad
- grid.7922.e0000 0001 0244 7875Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- grid.7922.e0000 0001 0244 7875Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand ,grid.512985.2FRS(T), The Royal Society of Thailand, Sanam Sueapa, Dusit, Bangkok, Thailand
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17
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Guest PC, Kesharwani P, Butler AE, Sahebkar A. The COVID-19 Pandemic: SARS-CoV-2 Structure, Infection, Transmission, Symptomology, and Variants of Concern. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1412:3-26. [PMID: 37378759 DOI: 10.1007/978-3-031-28012-2_1] [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
Since it was first detected in December 2019, the COVID-19 pandemic has spread across the world and affected virtually every country and territory. The pathogen driving this pandemic is SARS-CoV-2, a positive-sense single-stranded RNA virus which is primarily transmissible though the air and can cause mild to severe respiratory infections in humans. Within the first year of the pandemic, the situation worsened with the emergence of several SARS-CoV-2 variants. Some of these were observed to be more virulent with varying capacities to escape the existing vaccines and were, therefore, denoted as variants of concern. This chapter provides a general overview of the course of the COVID-19 pandemic up to April 2022 with a focus on the structure, infection, transmission, and symptomology of the SARS-CoV-2 virus. The main objectives were to investigate the effects of the variants of concern on the trajectory of the virus and to highlight a potential pathway for coping with the current and future pandemics.
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Affiliation(s)
- Paul C Guest
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Department of Psychiatry, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
- Laboratory of Translational Psychiatry, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Alexandra E Butler
- Research Department, Royal College of Surgeons in Ireland Bahrain, Adliya, Bahrain
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- School of Medicine, The University of Western Australia, Perth, WA, Australia
- Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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18
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Cocherie T, Zafilaza K, Leducq V, Marot S, Calvez V, Marcelin AG, Todesco E. Epidemiology and Characteristics of SARS-CoV-2 Variants of Concern: The Impacts of the Spike Mutations. Microorganisms 2022; 11:30. [PMID: 36677322 PMCID: PMC9866527 DOI: 10.3390/microorganisms11010030] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
SARS-CoV-2 expresses on its surface the Spike protein responsible for binding with the ACE2 receptor and which carries the majority of immunodominant epitopes. Mutations mainly affect this protein and can modify characteristics of the virus, giving each variant a unique profile concerning its transmissibility, virulence, and immune escape. The first lineage selected is the B.1 lineage characterized by the D614G substitution and from which all SARS-CoV-2 variants of concern have emerged. The first three variants of concern Alpha, Beta, and Gamma spread in early 2021: all shared the N501Y substitution. These variants were replaced by the Delta variant in summer 2021, carrying unique mutations like the L452R substitution and associated with higher virulence. It was in turn quickly replaced by the Omicron variant at the end of 2021, which has predominated since then, characterized by its large number of mutations. The successive appearance of variants of concern showed a dynamic evolution of SARS-CoV-2 through the selection and accumulation of mutations. This has not only allowed progressive improvement of the transmissibility of SARS-CoV-2, but has also participated in a better immune escape of the virus. This review brings together acquired knowledge about SARS-CoV-2 variants of concern and the impacts of the Spike mutations.
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Affiliation(s)
| | | | | | | | | | | | - Eve Todesco
- Institut Pierre Louis d’Épidémiologie et de Santé Publique (iPLESP), INSERM, Sorbonne Université, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Virologie, 75013 Paris, France
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19
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Moen LV, Vollan HS, Bråte J, Hungnes O, Bragstad K. Molecular Epidemiology of the Norwegian SARS-CoV-2 Delta Lineage AY.63. Viruses 2022; 14:v14122734. [PMID: 36560738 PMCID: PMC9781678 DOI: 10.3390/v14122734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022] Open
Abstract
Extensive genomic surveillance has given great insights into the evolution of the SARS-CoV-2 virus and emerging variants. During the summer months of 2021, Norway was dominated by the Pango lineage AY.63 which is a sub-lineage of the highly transmissible Delta variant. Strikingly, AY.63 did not spread in other countries to any significant extent. AY.63 carried a key mutation, A222V, in the spike protein, as well as the deletion of three residues in nsp1. Although these mutations are close to functionally important areas, we did not find any evidence that they induced higher fitness compared to other Delta lineages. This variant was introduced to Norway at a time when there were low levels of SARS-CoV-2 and contact-reducing measures were relaxed, which probably explains why the lineage rose so quickly. Furthermore, we found that the lack of imports of AY.63 from other countries probably led to the eventual demise of the lineage in Norway.
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20
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Garziano M, Utyro O, Strizzi S, Vanetti C, Saulle I, Conforti C, Cicilano F, Ardizzone F, Cappelletti G, Clerici M, Limanaqi F, Biasin M. Saliva and Plasma Neutralizing Activity Induced by the Administration of a Third bnt162b2 Vaccine Dose. Int J Mol Sci 2022; 23:ijms232214341. [PMID: 36430815 PMCID: PMC9693379 DOI: 10.3390/ijms232214341] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/22/2022] Open
Abstract
The BNT162b2 vaccine induces neutralizing activity (NA) in serum, but no data are available on whether a third-dose activates specific-immunity within the oral mucosa, representing the primary route of viral-entry. To carefully address this issue, we investigated if such immunity is boosted by SARS-CoV-2-infection; how long it is maintained over-time; and if it protects against the SARS-CoV-2 lineage B.1 (EU) and the emerging Delta and Omicron variants. NA was measured in plasma and saliva samples from: uninfected SARS-CoV-2-Vaccinated (SV), subjects infected prior to vaccination (SIV), and subjects who were infected after the second (SIV2) or the third (SIV3) vaccine dose. Samples were collected immediately before (T0), 15 days (T1), and 90 days (T2) post third-dose administration (SV and SIV), or 15 days post-infection (SIV2 and SIV3). In all the enrolled groups, NA in plasma and saliva: (i) was higher against EU compared to the other variants at all time-points (SV: T0 and T1, EU vs. both Delta and Omicron p < 0.001; T2 p < 0.01) (SIV: T0, EU vs. Delta p < 0.05; EU vs. Omi p < 0.01; T1 and T2 EU vs. Delta p < 0.01; EU vs. Omi p < 0.001); (ii) was boosted by the administration of the third dose; iii) declined over-time, albeit being detectable in almost all subjects at T2. The monitoring of NA over time will be important in clarifying if different NA levels may influence either acquisition or course of infection to properly plan the timing of a fourth vaccine dose administration.
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Affiliation(s)
- Micaela Garziano
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 20122 Milan, Italy
| | - Olga Utyro
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
| | - Sergio Strizzi
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
| | - Claudia Vanetti
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
| | - Irma Saulle
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 20122 Milan, Italy
| | - Chiara Conforti
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
| | - Federica Cicilano
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
| | - Francesco Ardizzone
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
| | - Gioia Cappelletti
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
| | - Mario Clerici
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 20122 Milan, Italy
- Don C. Gnocchi Foundation, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Foundation, Via A. Capecelatro 66, 20148 Milan, Italy
| | - Fiona Limanaqi
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 20122 Milan, Italy
| | - Mara Biasin
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
- Correspondence:
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21
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Nakashima N, Nakashima A, Nakashima K, Takano M. Olfactory marker protein contains a leucine-rich domain in the Ω-loop important for nuclear export. Mol Brain 2022; 15:89. [PMID: 36333725 PMCID: PMC9636679 DOI: 10.1186/s13041-022-00973-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/15/2022] [Indexed: 11/06/2022] Open
Abstract
Olfactory marker protein (OMP) is a cytosolic protein expressed in mature olfactory receptor neurons (ORNs). OMP modulates cAMP signalling and regulates olfactory sensation and axonal targeting. OMP is a small soluble protein, and passive diffusion between nucleus and cytoplasm is expected. However, OMP is mostly situated in the cytosol and is only sparsely detected in the nuclei of a subset of ORNs, hypothalamic neurons and heterologously OMP-expressing cultured cells. OMP can enter the nucleus in association with transcription factors. However, how OMP is retained in the cytosol at rest is unclear. Because OMP is proposed to affect cell differentiation, it is important to understand how OMP is distributed between cytoplasm and nucleus. To elucidate the structural profile of OMP, we applied several bioinformatics methods to a multiple sequence alignment (MSA) of OMP protein sequences and ranked the evolutionarily conserved residues. In addition to the previously reported cAMP-binding domain, we identified a leucine-rich domain in the Ω-loop of OMP. We introduced mutations into the leucine-rich region and heterologously expressed the mutant OMP in HEK293T cells. Mutations into alanine increased the nuclear distribution of OMP quantified by immunocytochemistry and western blotting. Therefore, we concluded that OMP contains a leucine-rich domain important for nuclear transport.
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Affiliation(s)
- Noriyuki Nakashima
- grid.410781.b0000 0001 0706 0776Department of Physiology, Kurume University School of Medicine, 67 Asahi-Machi, Kurume-Shi, Fukuoka 830-0011 Japan
| | - Akiko Nakashima
- grid.410781.b0000 0001 0706 0776Department of Physiology, Kurume University School of Medicine, 67 Asahi-Machi, Kurume-Shi, Fukuoka 830-0011 Japan
| | - Kie Nakashima
- grid.31432.370000 0001 1092 3077Department of Physiology and Cell Biology, Kobe University School of Medicine, 7-5-1 Kusunoki-Cho, Chuo-Ku, Kobe, 650-0017 Japan
| | - Makoto Takano
- grid.410781.b0000 0001 0706 0776Department of Physiology, Kurume University School of Medicine, 67 Asahi-Machi, Kurume-Shi, Fukuoka 830-0011 Japan
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22
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Zhang M, Zhang P, Liang Y, Du B, Li L, Yu Z, Wang H, Wang Q, Zhang X, Zhang W. A systematic review of current status and challenges of vaccinating children against SARS-CoV-2. J Infect Public Health 2022; 15:1212-1224. [PMID: 36257126 PMCID: PMC9557115 DOI: 10.1016/j.jiph.2022.10.006] [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: 05/30/2022] [Revised: 09/22/2022] [Accepted: 10/04/2022] [Indexed: 12/04/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has inflicted immense damage to countries, economies and societies worldwide. Authorized COVID-19 vaccines based on different platforms have been widely inoculated in adults, showing up to 100% immunogenicity with significant efficacy in preventing SARS-CoV-2 infections and the occurrence of severe COVID-19. It has also greatly slowed the evolution of SARS-CoV-2 variants, as shown in clinical trials and real-world evidence. However, the total dosage of COVID-19 vaccines for children is much smaller than that for adults due to limitations from parental concern of vaccine safety, presenting a potential obstacle in ending the COVID-19 pandemic. SARS-CoV-2 not only increases the risk of severe multisystem inflammatory syndrome (MIS-C) in children, but also negatively affects children's psychology and academics, indirectly hindering the maintenance and progress of normal social order. Therefore, this article examines the clinical manifestations of children infected with SARS-CoV-2, the status of vaccination against COVID-19 in children, vaccination-related adverse events, and the unique immune mechanisms of children. In particular, the necessity and challenges of vaccinating children against SARS-CoV-2 were highlighted from the perspectives of society and family. In summary, parental hesitancy is unnecessary as adverse events after COVID-19 vaccination have been proven to be infrequent, comprise of mild symptoms, and have a good prognosis.
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Affiliation(s)
- Mengxin Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Pin Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Ying Liang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Bang Du
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Lifeng Li
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Zhidan Yu
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Huanmin Wang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Qionglin Wang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China.
| | - Xianwei Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China.
| | - Wancun Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China.
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23
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Dehghani J, Movafeghi A, Mathieu-Rivet E, Mati-Baouche N, Calbo S, Lerouge P, Bardor M. Microalgae as an Efficient Vehicle for the Production and Targeted Delivery of Therapeutic Glycoproteins against SARS-CoV-2 Variants. Mar Drugs 2022; 20:md20110657. [PMID: 36354980 PMCID: PMC9698596 DOI: 10.3390/md20110657] [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: 09/25/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/27/2022] Open
Abstract
Severe acute respiratory syndrome–Coronavirus 2 (SARS-CoV-2) can infect various human organs, including the respiratory, circulatory, nervous, and gastrointestinal ones. The virus is internalized into human cells by binding to the human angiotensin-converting enzyme 2 (ACE2) receptor through its spike protein (S-glycoprotein). As S-glycoprotein is required for the attachment and entry into the human target cells, it is the primary mediator of SARS-CoV-2 infectivity. Currently, this glycoprotein has received considerable attention as a key component for the development of antiviral vaccines or biologics against SARS-CoV-2. Moreover, since the ACE2 receptor constitutes the main entry route for the SARS-CoV-2 virus, its soluble form could be considered as a promising approach for the treatment of coronavirus disease 2019 infection (COVID-19). Both S-glycoprotein and ACE2 are highly glycosylated molecules containing 22 and 7 consensus N-glycosylation sites, respectively. The N-glycan structures attached to these specific sites are required for the folding, conformation, recycling, and biological activity of both glycoproteins. Thus far, recombinant S-glycoprotein and ACE2 have been produced primarily in mammalian cells, which is an expensive process. Therefore, benefiting from a cheaper cell-based biofactory would be a good value added to the development of cost-effective recombinant vaccines and biopharmaceuticals directed against COVID-19. To this end, efficient protein synthesis machinery and the ability to properly impose post-translational modifications make microalgae an eco-friendly platform for the production of pharmaceutical glycoproteins. Notably, several microalgae (e.g., Chlamydomonas reinhardtii, Dunaliella bardawil, and Chlorella species) are already approved by the U.S. Food and Drug Administration (FDA) as safe human food. Because microalgal cells contain a rigid cell wall that could act as a natural encapsulation to protect the recombinant proteins from the aggressive environment of the stomach, this feature could be used for the rapid production and edible targeted delivery of S-glycoprotein and soluble ACE2 for the treatment/inhibition of SARS-CoV-2. Herein, we have reviewed the pathogenesis mechanism of SARS-CoV-2 and then highlighted the potential of microalgae for the treatment/inhibition of COVID-19 infection.
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Affiliation(s)
- Jaber Dehghani
- Université de Rouen Normandie, Laboratoire GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, F-76000 Rouen, France
| | - Ali Movafeghi
- Department of Plant, Cell and Molecular Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz 5166616471, Iran
| | - Elodie Mathieu-Rivet
- Université de Rouen Normandie, Laboratoire GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, F-76000 Rouen, France
| | - Narimane Mati-Baouche
- Université de Rouen Normandie, Laboratoire GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, F-76000 Rouen, France
| | - Sébastien Calbo
- Université de Rouen Normandie, Inserm U1234, F-76000 Rouen, France
| | - Patrice Lerouge
- Université de Rouen Normandie, Laboratoire GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, F-76000 Rouen, France
| | - Muriel Bardor
- Université de Rouen Normandie, Laboratoire GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, F-76000 Rouen, France
- Correspondence: ; Tel.: +33-2-35-14-67-51
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24
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Chen Q, Zhang J, Wang P, Zhang Z. The mechanisms of immune response and evasion by the main SARS-CoV-2 variants. iScience 2022; 25:105044. [PMID: 36068846 PMCID: PMC9436868 DOI: 10.1016/j.isci.2022.105044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic. SARS-CoV-2 carries a unique group of mutations, and the transmission of the virus has led to the emergence of other mutants such as Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Kappa (B.1.617.1), Delta (B.1.617.2) and Omicron (B.1.1.529). The advent of a vaccine has raised hopes of ending the pandemic. However, the mutation variants of SARS-CoV-2 have raised concerns about the effectiveness of vaccines because the data showed that the vaccine was less effective against mutation variants compared to the previous variants. Mutation variants could easily mutate the N-segment structure and receptor domain of its spike glycoprotein (S) protein to escape antibody recognition. Therefore, it is vital to understand the potential immune response and evasion mechanism of SARS-CoV-2 variants. In this review, immune response and evasion mechanisms of several SARS-CoV-2 variants are described, which could provide some helpful advice for future vaccines.
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Affiliation(s)
- Qiuli Chen
- Department of Research and Development, Zhejiang Zhongwei Medical Research Center, Hangzhou, Zhejiang 310018, China
| | - Jiawei Zhang
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Peter Wang
- Department of Research and Development, Zhejiang Zhongwei Medical Research Center, Hangzhou, Zhejiang 310018, China
| | - Zuyong Zhang
- The Affiliated Hangzhou Xixi Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310023, China
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25
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Bobrin V, Chen SPR, Grandes Reyes CF, Smith T, Purcell DFJ, Armstrong J, McAuley JL, Monteiro MJ. Surface Inactivation of Highly Mutated SARS-CoV-2 Variants of Concern: Alpha, Delta, and Omicron. Biomacromolecules 2022; 23:3960-3967. [PMID: 35994316 PMCID: PMC9454278 DOI: 10.1021/acs.biomac.2c00801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/04/2022] [Indexed: 11/28/2022]
Abstract
Continued SARS-CoV-2 transmission among the human population has meant the evolution of the virus to produce variants of increased infectiousness and virulence, coined variants of concern (VOCs). The last wave of pandemic infections was driven predominantly by the delta VOC, but because of continued transmission and adaptive mutations, the more highly transmissible omicron variant emerged and is now dominant. However, due to waning immunity and emergence of new variants, vaccines alone cannot control the pandemic. The application of an antiviral coating to high-touch surfaces and physical barriers such as masks are an effective means to inactivate the virus and their spread. Here, we demonstrate an environmentally friendly water-borne polymer coating that can completely inactivate SARS-CoV-2 independent of the infectious variant. The polymer was designed to target the highly glycosylated spike protein on the virion surface and inactivate the virion by disruption of the viral membrane through a nano-mechanical process. Our findings show that, even with low amounts of coating on the surface (1 g/m2), inactivation of alpha, delta, and omicron VOCs and degradation of their viral genome were complete. Furthermore, our data shows that the polymer induces little to no skin sensitization in mice and is non-toxic upon oral ingestion in rats. We anticipate that our transparent polymer coating can be applied to face masks and many other surfaces to capture and inactivate the virus, aiding in the reduction of SARS-CoV-2 transmission and evolution of new variants of concern.
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Affiliation(s)
- Valentin
A. Bobrin
- Australian
Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sung-Po R. Chen
- Australian
Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Tim Smith
- Department
of Microbiology and Immunology, The University
of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Damian F. J. Purcell
- Department
of Microbiology and Immunology, The University
of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Jason Armstrong
- Boeing
Research and Technology Australia, Level 2, Hawken building (50), Staff House Rd, Brisbane, QLD 4072, Australia
| | - Julie L. McAuley
- Department
of Microbiology and Immunology, The University
of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Michael J. Monteiro
- Australian
Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
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Mahmood TB, Hossan MI, Mahmud S, Shimu MSS, Alam MJ, Bhuyan MMR, Emran TB. Missense mutations in spike protein of SARS‐CoV‐2 delta variant contribute to the alteration in viral structure and interaction with hACE2 receptor. Immun Inflamm Dis 2022; 10:e683. [PMID: 36039645 PMCID: PMC9382871 DOI: 10.1002/iid3.683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 07/17/2022] [Accepted: 07/22/2022] [Indexed: 11/11/2022] Open
Abstract
Introduction Many of the global pandemics threaten human existence over the decades among which coronavirus disease (COVID‐19) is the newest exposure circulating worldwide. The RNA encoded severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) virus is referred as the pivotal agent of this deadly disease that induces respiratory tract infection by interacting host ACE2 receptor with its spike glycoprotein. Rapidly evolving nature of this virus modified into new variants helps in perpetrating immune escape and protection against host defense mechanism. Consequently, a new isolate, delta variant originated from India is spreading perilously at a higher infection rate. Methods In this study, we focused to understand the conformational and functional significance of the missense mutations found in the spike glycoprotein of SARS‐CoV‐2 delta variant performing different computational analysis. Results From physiochemical analysis, we found that the acidic isoelectric point of the virus elevated to basic pH level due to the mutations. The targeted mutations were also found to change the interactive bonding pattern and conformational stability analyzed by the molecular dynamic's simulation. The molecular docking study also revealed that L452R and T478K mutations found in the RBD domain of delta variant spike protein contributed to alter interaction with the host ACE2 receptor. Conclusions Overall, this study provided insightful evidence to understand the morphological and attributive impact of the mutations on SARS‐CoV‐2 delta variant.
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Affiliation(s)
- Tousif Bin Mahmood
- Department of Biotechnology and Genetic Engineering Noakhali Science and Technology University Noakhali Bangladesh
| | - Mohammad Imran Hossan
- Department of Biotechnology and Genetic Engineering Noakhali Science and Technology University Noakhali Bangladesh
| | - Shafi Mahmud
- Department of Genetic Engineering and Biotechnology University of Rajshahi Rajshahi Bangladesh
| | | | - Md. Jahidul Alam
- Department of Applied Chemistry and Chemical Engineering Noakhali Science and Technology University Noakhali Bangladesh
| | - Md. Mahfuzur Rahman Bhuyan
- Department of Biochemistry and Molecular Biology Noakhali Science and Technology University Noakhali Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy BGC Trust University Bangladesh Chittagong Bangladesh
- Department of Pharmacy Faculty of Allied Health Sciences, Daffodil International University Dhaka Bangladesh
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Vakil MK, Mansoori Y, Al‐Awsi GRL, Hosseinipour A, Ahsant S, Ahmadi S, Ekrahi M, Montaseri Z, Pezeshki B, Mohaghegh P, Sohrabpour M, Bahmanyar M, Daraei A, Dadkhah Jouybari T, Tavassoli A, Ghasemian A. Individual genetic variability mainly of Proinflammatory cytokines, cytokine receptors, and toll-like receptors dictates pathophysiology of COVID-19 disease. J Med Virol 2022; 94:4088-4096. [PMID: 35538614 PMCID: PMC9348290 DOI: 10.1002/jmv.27849] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 11/12/2022]
Abstract
Innate and acquired immunity responses are crucial for viral infection elimination. However, genetic variations in coding genes may exacerbate the inflammation or initiate devastating cytokine storms which poses severe respiratory conditions in coronavirus disease-19 (COVID-19). Host genetic variations in particular those related to the immune responses determine the patients' susceptibility and COVID-19 severity and pathophysiology. Gene polymorphisms such as single nucleotide polymorphisms (SNPs) of interferons, TNF, IL1, IL4, IL6, IL7, IL10, and IL17 predispose patients to the severe form of COVID-19 or severe acute respiratory syndrome coronavirus-2 (SARS-COV-2). These variations mainly alter the gene expression and cause a severe response by B cells, T cells, monocytes, neutrophils, and natural killer cells participating in a cytokine storm. Moreover, cytokines and chemokines SNPs are associated with the severity of COVID-19 and clinical outcomes depending on the corresponding effect. Additionally, genetic variations in genes encoding toll-like receptors (TLRs) mainly TLR3, TLR7, and TLR9 have been related to the COVID-19 severe respiratory symptoms. The specific relation of these mutations with the novel variants of concern (VOCs) infection remains to be elucidated. Genetic variations mainly within genes encoding proinflammatory cytokines, cytokine receptors, and TLRs predispose patients to COVID-19 disease severity. Understanding host immune gene variations associated with the SARS-COV-2 infection opens insights to control the pathophysiology of emerging viral infections.
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Affiliation(s)
- Mohammad Kazem Vakil
- Noncommunicable Diseases Research CenterFasa University of Medical SciencesFasaIran
| | - Yaser Mansoori
- Noncommunicable Diseases Research CenterFasa University of Medical SciencesFasaIran
| | - Ghaidaa Raheem Lateef Al‐Awsi
- University of Al‐QadisiyahCollege of ScienceAl DiwaniyahIraq
- Department of Radiological TechniquesAl‐Mustaqbal University CollegeBabylonIraq
| | - Ali Hosseinipour
- Department of Internal MedicineFasa University of Medical SciencesFasaIran
| | - Samaneh Ahsant
- Noncommunicable Diseases Research CenterFasa University of Medical SciencesFasaIran
| | - Sedigheh Ahmadi
- Noncommunicable Diseases Research CenterFasa University of Medical SciencesFasaIran
| | - Mohammad Ekrahi
- Noncommunicable Diseases Research CenterFasa University of Medical SciencesFasaIran
| | - Zahra Montaseri
- Department of Infectious DiseasesFasa University of Medical SciencesFasaIran
| | - Babak Pezeshki
- Noncommunicable Diseases Research CenterFasa University of Medical SciencesFasaIran
| | - Poopak Mohaghegh
- Pediatrics Department, School of MedicineFasa University of Medical SciencesFasaIran
| | - Mojtaba Sohrabpour
- Noncommunicable Diseases Research CenterFasa University of Medical SciencesFasaIran
| | - Maryam Bahmanyar
- Pediatrics Department, School of MedicineFasa University of Medical SciencesFasaIran
| | - Abdolreza Daraei
- Department of Medical Genetics, School of MedicineBabol University of Medical SciencesBabolIran
| | | | | | - Abdolmajid Ghasemian
- Noncommunicable Diseases Research CenterFasa University of Medical SciencesFasaIran
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Abidi M, Soheilifard R, Ghasemi RH. Comparison of the unbinding process of RBD-ACE2 complex between SARS-CoV-2 variants (Delta, delta plus, and Lambda): A steered molecular dynamics simulation. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2114599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Mohadese Abidi
- Department of Mechanical Engineering, Hakim Sabzevari University, Sabzevar, Iran
| | - Reza Soheilifard
- Department of Mechanical Engineering, Hakim Sabzevari University, Sabzevar, Iran
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Devadoss D, Acharya A, Manevski M, Houserova D, Cioffi MD, Pandey K, Nair M, Chapagain P, Mirsaeidi M, Borchert GM, Byrareddy SN, Chand HS. Immunomodulatory LncRNA on antisense strand of ICAM-1 augments SARS-CoV-2 infection-associated airway mucoinflammatory phenotype. iScience 2022; 25:104685. [PMID: 35789750 PMCID: PMC9242679 DOI: 10.1016/j.isci.2022.104685] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/25/2022] [Accepted: 06/23/2022] [Indexed: 01/20/2023] Open
Abstract
Noncoding RNAs are important regulators of mucoinflammatory response, but little is known about the contribution of airway long noncoding RNAs (lncRNAs) in COVID-19. RNA-seq analysis showed a more than 4-fold increased expression of IL-6, ICAM-1, CXCL-8, and SCGB1A1 inflammatory factors; MUC5AC and MUC5B mucins; and SPDEF, FOXA3, and FOXJ1 transcription factors in COVID-19 patient nasal samples compared with uninfected controls. A lncRNA on antisense strand to ICAM-1 or LASI was induced 2-fold in COVID-19 patients, and its expression was directly correlated with viral loads. A SARS-CoV-2-infected 3D-airway model largely recapitulated these clinical findings. RNA microscopy and molecular modeling indicated a possible interaction between viral RNA and LASI lncRNA. Notably, blocking LASI lncRNA reduced the SARS-CoV-2 replication and suppressed MUC5AC mucin levels and associated inflammation, and select LASI-dependent miRNAs (e.g., let-7b-5p and miR-200a-5p) were implicated. Thus, LASI lncRNA represents an essential facilitator of SARS-CoV-2 infection and associated airway mucoinflammatory response.
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Affiliation(s)
- Dinesh Devadoss
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Marko Manevski
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Dominika Houserova
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Michael D. Cioffi
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Kabita Pandey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Madhavan Nair
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Mehdi Mirsaeidi
- Miller School of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, University of Miami, Miami, FL 33136, USA
| | - Glen M. Borchert
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Hitendra S. Chand
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
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Madasu PK, Maity A, Ghosh SK, Chandran T. Insights into the microevolution of SARS-ACE2 interactions: in silico analysis of glycosylation and SNP pattern. J Biomol Struct Dyn 2022:1-8. [PMID: 35930333 DOI: 10.1080/07391102.2022.2106517] [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: 10/16/2022]
Abstract
The prefatory protein-glycan interaction and stabilizing protein-protein interaction of severe acute respiratory syndrome viruses with angiotensin-converting enzyme 2 play a significant role in complex formation thereby promoting endocytosis. The microevolution of SARS-CoV-2 over a period of time has a significant role in increasing the affinity of receptor-binding domain against angiotensin converting-enzyme 2. In this study, we have corroborated the vitality of acquired SNPs over a period of time with increased affinity by using docking studies. The results indicate that the virus modulates the undesirable glycosylation sites by a series of substitution and deletion mutations. It uses bulky residues such as Tyr/Phe for dynamic arrest for quick stabilization of the complex, and Lys residues for stabilizing via hydrogen bond formation besides increasing the binding affinity to ease the cell entry.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pavan K Madasu
- Department of Biotechnology, National Institute of Technology, Warangal, India
| | - Arpita Maity
- Department of Biotechnology, National Institute of Technology, Warangal, India
| | - Surya K Ghosh
- Department of Physics, National Institute of Technology, Warangal, India
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Pondé RAA. Physicochemical effect of the N501Y, E484K/Q, K417N/T, L452R and T478K mutations on the SARS-CoV-2 spike protein RBD and its influence on agent fitness and on attributes developed by emerging variants of concern. Virology 2022; 572:44-54. [PMID: 35580380 PMCID: PMC9096574 DOI: 10.1016/j.virol.2022.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/26/2022] [Accepted: 05/06/2022] [Indexed: 01/17/2023]
Abstract
The spike protein comprises one of the main structural components of SARS-CoV-2 because it is directly involved in the infection process and viral transmission, and also because of its immunogenic properties, as an inducer of the protective antibodies production and as a vaccine component. The occurrence of mutations in this region or in other the virus genome regions, comprises a natural phenomenon in its evolution. However, they also occur due to the selective immune pressure, to which the agent is continuously subjected, especially in the spike protein immunodominant regions, such as the RBD. Mutations in the spike protein can change the virus' fitness, increasing its affinity for target cells, its transmissibility and its virulence. In addition, these mutations can giving it the potential ability to evade the protective antibodies action obtained from convalescent sera or vaccine origin, as well as those used in therapy, which may favor the virus expansion and compromise the infection control. Five mutations N501Y, E484K/Q, K417N/T, L452R and T478K, located in the spike protein RBD, have had a greater impact because they are associated with new attributes developed by the virus, which characterize the emerging variants of concern (VOCs) of SARS-Cov-2 identified so far. The occurrence of these mutations induces complex physicochemical effects that can alter the spike protein's structure and its function, which in turn, lead to changes in the agents' fitness. This manuscript discusses the attributes of VOCs associated with the physicochemical effects caused by the aforementioned mutations.
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Affiliation(s)
- R A A Pondé
- State Department of Health SES/Superintendence of Health Surveillance SUVISA/GO, Management of Epidemiological Surveillance-GVE/Coordination of Analysis and Research-CAP, Goiânia, Goiás, Brazil; Laboratory of Human Virology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil.
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32
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Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 101:105282. [PMID: 35427787 PMCID: PMC9005225 DOI: 10.1016/j.meegid.2022.105282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 02/07/2023]
Abstract
Background The massive increase in COVID-19 infection had generated a second wave in India during May–June 2021 with a critical pandemic situation. The Delta variant (B.1.617.2) was a significant factor during the second wave. Conversely, the UK had passed through the crucial phase of the pandemic from November to December 2020 due to B.1.1.7. The study tried to comprehend the pandemic response in the UK and India to the spread of the B.1.1.7 (Alpha, UK) variant and B.1.617.2 (Delta, India) variant. Methods This study was performed in three directions to understand the pandemic response of the two emerging variants. First, we served comparative genomics, such as genome sequence submission patterns, mutational landscapes, and structural landscapes of significant mutations (N501Y, D614G, L452R, E484Q, and P681R). Second, we performed evolutionary epidemiology using molecular phylogenetics, scatter plots of the cluster evaluation, country-wise transmission pattern, and frequency pattern. Third, the receptor binding pattern was analyzed using the Wuhan reference strain and the other two variants. Results The study analyzed the country-wise and region-wise genome sequences and their submission pattern, molecular phylogenetics, scatter plot of the cluster evaluation, country-wise geographical distribution and transmission pattern, frequency pattern, entropy diversity, and mutational landscape of the two variants. The structural pattern was analyzed in the N501Y, D614G L452R, E484Q, and P681R mutations. The study found increased molecular interactivity between hACE2-RBD binding of B.1.1.7 and B.1.617.2 compared to the Wuhan reference strain. Our receptor binding analysis showed a similar indication pattern for hACE2-RBD of these two variants. However, B.1.617.2 offers slightly better stability in the hACE2-RBD binding pattern through MD simulation than B.1.1.7. Conclusion The increased hACE2-RBD binding pattern of B.1.1.7 and B.1.617.2 might help to increase the infectivity compared to the Wuhan reference strain.
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Tahsin A, Ahmed R, Bhattacharjee P, Adiba M, Al Saba A, Yasmin T, Chakraborty S, Hasan AM, Nabi AN. Most frequently harboured missense variants of hACE2 across different populations exhibit varying patterns of binding interaction with spike glycoproteins of emerging SARS-CoV-2 of different lineages. Comput Biol Med 2022; 148:105903. [PMID: 35932731 PMCID: PMC9296255 DOI: 10.1016/j.compbiomed.2022.105903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 07/03/2022] [Accepted: 07/16/2022] [Indexed: 11/22/2022]
Abstract
Since the emergence of SARS-CoV-2 at Wuhan in the Hubei province of China in 2019, the virus has accumulated various mutations, giving rise to many variants. According to the combinations of mutations acquired, these variants are classified into lineages and greatly differ in infectivity and transmissibility. In 2021 alone, a variant of interest (VoI) Mu (B.1.621), as well as, variants of concern (VoC) Delta (B.1.617.2) and Omicron (BA.1, BA.2) and later in 2022, BA.4, BA.5, and BA.2.12.1 have emerged. Since then, the world has seen prominent surges in the rate of infection during short periods of time. However, not all populations have suffered equally, which suggests a possible role of host genetic factors. Here, we investigated the strength of binding of the spike glycoprotein receptor-binding domain (RBD) of the SARS-CoV-2 variants: Mu, Delta, Delta Plus (AY.1), Omicron sub-variants BA.1, BA.2, BA.4, BA.5, and BA.2.12.1 with the human angiotensin-converting enzyme 2 (hACE2) missense variants prevalent in major populations. In this purpose, molecular docking analysis, as well as, molecular dynamics simulation was performed of the above-mentioned SARS-CoV-2 RBD variants with the hACE2 containing the single amino acid substitutions prevalent in African (E37K), Latin American (F40L), non-Finnish European (D355 N), and South Asian (P84T) populations, in order to predict the effects of the lineage-defining mutations of the viral variants on receptor binding. The effects of these mutations on protein stability were also explored. The protein-protein docking and molecular dynamics simulation analyses have revealed variable strength of attachment and exhibited altered interactions in the case of different hACE2-RBD complexes. In vitro studies are warranted to confirm these findings which may enable early prediction regarding the risk of transmissibility of newly emerging variants across different populations in the future.
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K A, Sharma A, Kumar D, Singh SK, Gupta G, Chellappan DK, Dua K, Nagraik R. Molecular aspects of Omicron, vaccine development, and recombinant strain XE: A review. J Med Virol 2022; 94:4628-4643. [PMID: 35705439 PMCID: PMC9349635 DOI: 10.1002/jmv.27936] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/02/2022] [Accepted: 06/14/2022] [Indexed: 12/19/2022]
Abstract
The global pandemic of COVID‐19 began in December 2019 and is still continuing. The past 2 years have seen the emergence of several variants that were more vicious than each other. The emergence of Omicron (B.1.1.529) proved to be a huge epidemiological concern as the rate of infection of this particular strain was enormous. The strain was identified in South Africa on November 24, 2021 and was classified as a “Variant of Concern” on November 26, 2021. The Omicron variant possessed mutations in the key RBD region, the S region, thereby increasing the affinity of ACE2 for better transmission of the virus. Antibody resistance was found in this variant and it was able to reduce vaccine efficiency of vaccines. The need for a booster vaccine was brought forth due to the prevalence of the Omicron variant and, subsequently, this led to targeted research and development of variant‐specific vaccines and booster dosage. This review discusses broadly the genomic characters and features of Omicron along with its specific mutations, evolution, antibody resistance, and evasion, utilization of CRISPR‐Cas12a assay for Omicron detection, T‐cell immunity elicited by vaccines against Omicron, and strategies to decrease Omicron infection along with COVID‐19 and it also discusses on XE recombinant variant and on infectivity of BA.2 subvariant of Omicron.
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Affiliation(s)
- Akash K
- School of Bioengineering and Food Technology, Faculty of Applied Sciences and BiotechnologyShoolini UniversitySolanHimachal PradeshIndia
| | - Avinash Sharma
- School of Bioengineering and Food Technology, Faculty of Applied Sciences and BiotechnologyShoolini UniversitySolanHimachal PradeshIndia
| | - Deepak Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical SciencesShoolini UniversitySolanHimachal PradeshIndia
| | - Sachin K. Singh
- School of Pharmaceutical SciencesLovely Professional UniversityPhagwara, PunjabIndia
| | - Gaurav Gupta
- School of PharmacySuresh Gyan Vihar UniversityJagatpura, JaipurIndia
- Uttaranchal Institute of Pharmaceutical SciencesUttaranchal UniversityDehradunIndia
- Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical SciencesSaveetha UniversityChennaiIndia
| | | | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary and Integrative MedicineUniversity of Technology SydneyUltimoNSWAustralia
- Discipline of Pharmacy Graduate School of HealthUniversity of Technology SydneyUltimoNSWAustralia
| | - Rupak Nagraik
- School of Bioengineering and Food Technology, Faculty of Applied Sciences and BiotechnologyShoolini UniversitySolanHimachal PradeshIndia
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Ebrahimi M, Karami L, Alijanianzadeh M. Computational repurposing approach for targeting the critical spike mutations in B.1.617.2 (delta), AY.1 (delta plus) and C.37 (lambda) SARS-CoV-2 variants using exhaustive structure-based virtual screening, molecular dynamic simulations and MM-PBSA methods. Comput Biol Med 2022; 147:105709. [PMID: 35728285 PMCID: PMC9170597 DOI: 10.1016/j.compbiomed.2022.105709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/03/2022] [Accepted: 06/04/2022] [Indexed: 11/26/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the contagious coronavirus disease 2019 (COVID-19) which was first identified in Wuhan, China, in December 2019. Around the world, many researchers focused their research on identifying inhibitors against the druggable SARS-CoV-2 targets. The reported genomic mutations have a direct effect on the receptor-binding domain (RBD), which interacts with host angiotensin-converting enzyme 2 (ACE-2) for viral cell entry. These mutations, some of which are variants of concern (VOC), lead to increased morbidity and mortality rates. The newest variants including B.1.617.2 (Delta), AY.1 (Delta plus), and C.37 (Lambda) were considered in this study. Thus, an exhaustive structure-based virtual screening of a ligand library (in which FDA approved drugs are also present) using the drug-likeness screening, molecular docking, ADMET profiling was performed followed by molecular dynamics (MD) simulation, and Molecular Mechanics-Poisson Boltzmann Surface Area (MM-PBSA) calculation to identify compounds or drugs can be repurposed for inhibiting the wild type, Delta, Delta plus and Lambda variants of RBD of the spike protein. Based on the virtual screening steps, two FDA approved drugs, Atovaquone (atv) and Praziquantel (prz), were selected and repurposed as the best candidates of SARS-CoV-2 RBD inhibitors. Molecular docking results display that both atv and prz contribute in different interaction with binding site residues (Gln493, Asn501 and Gly502 in the hydrogen bond formation, Phe490 and Tyr505 in the π- π stacking and Tyr449, Ser494, and Phe497 in the vdW interactions) in the wild type, Delta, Delta plus and Lambda variants of RBD of the spike protein. MD simulations revealed that among the eight studied complexes, the wild type-atv and Delta-prz complexes have the most structural stability over the simulation time. Furthermore, MM-PBSA calculation showed that in the atv containing complexes, highest binding affinity is related to the wild type-atv complex and in the prz containing complexes, it is related to the Delta-prz complex. The validation of docking results was done by comparing with experimental data (heparin in complex with wild type and Delta variants). Also, comparison of the obtained results with the result of simulation of the k22 with the studied proteins showed that atv and prz are suitable inhibitors for these proteins, especially wild type t and Delta variant, respectively. Thus, we found that atv and prz are the best candidate for inhibition of wild type and Delta variant of the spike protein. Also, atv can be an appropriate inhibitor for the Lambda variant. Obtained in silico results may help the development of new anti-COVID-19 drugs.
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Affiliation(s)
- Maryam Ebrahimi
- Department of Plant Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Leila Karami
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
| | - Mahdi Alijanianzadeh
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
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Chakraborty C, Sharma AR, Bhattacharya M, Agoramoorthy G, Lee SS. A Paradigm Shift in the Combination Changes of SARS-CoV-2 Variants and Increased Spread of Delta Variant (B.1.617.2) across the World. Aging Dis 2022; 13:927-942. [PMID: 35656100 PMCID: PMC9116911 DOI: 10.14336/ad.2021.1117] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/17/2021] [Indexed: 12/13/2022] Open
Abstract
Since September 2020, the SARS-CoV-2 variants have gained their dominance worldwide, especially in Kenya, Italy, France, the UK, Turkey, Indonesia, India, Finland, Ireland, Singapore, Denmark, Germany, and Portugal. In this study, we developed a model on the frequency of delta variants across 28 countries (R2= 0.1497), displaying the inheritance of mutations during the generation of the delta variants with 123,526 haplotypes. The country-wise haplotype network showed the distribution of haplotypes in USA (10,174), Denmark (5,637), India (4,089), Germany (2,350), Netherlands (1,899), Sweden (1,791), Italy (1,720), France (1,293), Ireland (1,257), Belgium (1,207), Singapore (1,193), Portugal (1,184) and Spain (1,133). Our analysis shows the highest haplotype in Europe with 84% and the lowest in Australia with 0.00001%. A model of scatter plot was generated with a regression line which provided the estimated rate of mutation, including 24.048 substitutions yearly. Our study concluded that the high global prevalence of the delta variants is due to a high frequency of infectivity, supporting the paradigm shift of the viral variants.
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Affiliation(s)
- Chiranjib Chakraborty
- 1Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India
| | - Ashish Ranjan Sharma
- 2Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Gangwon-do, Korea
| | | | | | - Sang-Soo Lee
- 2Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Gangwon-do, Korea
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Ranjan P, Neha, Devi C, Devar KA, Das P. The influence of new SARS-CoV-2 variant Omicron (B.1.1.529) on vaccine efficacy, its correlation to Delta variants: A computational approach. Microb Pathog 2022; 169:105619. [PMID: 35690234 PMCID: PMC9174103 DOI: 10.1016/j.micpath.2022.105619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 05/28/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022]
Abstract
The newly discovered COVID variant B.1.1.529 in Botswana has more than 30 mutations in spike and many other in non-spike proteins, far more than any other SARS-CoV-2 variant accepted as a variant of concern by the WHO and officially named Omicron, and has sparked concern among scientists and the general public. Our findings provide insights into structural modification caused by the mutations in the Omicrons receptor-binding domain and look into the effects on interaction with the hosts neutralizing antibodies CR3022, B38, CB6, P2B–2F6, and REGN, as well as ACE2R using an in silico approach. Computational analysis revealed that the Omicron variant has a higher binding affinity for the human ACE2 receptor than the wild and Delta (AY.1 and AY.2 strains), but lower than the Delta AY.3 strain. MD simulation and docking analysis suggest that the omicron and Delta AY.3 were found to have relatively unstable RBD structures and hampered interactions with antibodies more than wild and Delta (AY.1 and AY.2), which may lead to relatively more pathogenicity and antibody escape. In addition, we observed lower binding affinity of Omicron for human monoclonal antibodies (CR3022, B38, CB6, and P2B2F6) when compared to wild and Delta (AY.1 & AY.2). However, the binding affinity of Omicron RBD variants for CR3022, B38, and P2B2F6 antibodies is lower as compared to Delta AY.3, which might promote immune evasion and reinfection and needs further experimental investigation.
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Golcuk M, Hacisuleyman A, Yilmaz SZ, Taka E, Yildiz A, Gur M. SARS-CoV-2 Delta Variant Decreases Nanobody Binding and ACE2 Blocking Effectivity. J Chem Inf Model 2022; 62:2490-2498. [PMID: 35533364 PMCID: PMC9113008 DOI: 10.1021/acs.jcim.1c01523] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The Delta variant spreads more rapidly than previous variants of SARS-CoV-2. This variant comprises several mutations on the receptor-binding domain (RBDDelta) of its spike glycoprotein, which binds to the peptidase domain (PD) of angiotensin-converting enzyme 2 (ACE2) receptors in host cells. The RBD-PD interaction has been targeted by antibodies and nanobodies to prevent viral infection, but their effectiveness against the Delta variant remains unclear. Here, we investigated RBDDelta-PD interactions in the presence and absence of nanobodies H11-H4, H11-D4, and Ty1 by performing 21.8 μs of all-atom molecular dynamics simulations. Unbiased simulations revealed that Delta variant mutations strengthen RBD binding to ACE2 by increasing the hydrophobic interactions and salt bridge formation, but weaken interactions with H11-H4, H11-D4, and Ty1. Among these nanobodies H11-H4 and H11-D4 bind RBD without overlapping ACE2. They were unable to dislocate ACE2 from RBDDelta when bound side by side with ACE2 on RBD. Steered molecular dynamics simulations at comparable loading rates to high-speed atomic force microscopy (AFM) experiments estimated lower rupture forces of the nanobodies from RBDDelta compared to ACE2. Our results suggest that existing nanobodies are less effective to inhibit RBDDelta-PD interactions and a new generation of nanobodies is needed to neutralize the Delta variant.
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Affiliation(s)
- Mert Golcuk
- Department of Mechanical Engineering, Istanbul Technical University (ITU), 34437 Istanbul, Turkey
| | - Aysima Hacisuleyman
- Institute of Bioengineering, Swiss Federal Institute of Technology (EPFL), 1015 Lausanne, Switzerland
| | - Sema Zeynep Yilmaz
- Department of Mechanical Engineering, Istanbul Technical University (ITU), 34437 Istanbul, Turkey
| | - Elhan Taka
- Department of Mechanical Engineering, Istanbul Technical University (ITU), 34437 Istanbul, Turkey
| | - Ahmet Yildiz
- Physics Department, University of California, Berkeley, California 94720, United States.,Department of Molecular and Cellular Biology, University of California, Berkeley, California 94720, United States
| | - Mert Gur
- Department of Mechanical Engineering, Istanbul Technical University (ITU), 34437 Istanbul, Turkey
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Zhang B, Tian J, Zhang Q, Xie Y, Wang K, Qiu S, Lu K, Liu Y. Comparing the Nucleocapsid Proteins of Human Coronaviruses: Structure, Immunoregulation, Vaccine, and Targeted Drug. Front Mol Biosci 2022; 9:761173. [PMID: 35573742 PMCID: PMC9099148 DOI: 10.3389/fmolb.2022.761173] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 03/28/2022] [Indexed: 01/08/2023] Open
Abstract
The seven pathogenic human coronaviruses (HCoVs) include HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1, which usually cause mild upper respiratory tract diseases, and SARS-CoV, MERS-CoV, and SARS-CoV-2, which cause a severe acute respiratory syndrome. The nucleocapsid (N) protein, as the dominant structural protein from coronaviruses that bind to the genomic RNA, participates in various vital activities after virus invasion and will probably become a promising target of antiviral drug design. Therefore, a comprehensive literature review of human coronavirus’ pathogenic mechanism and therapeutic strategies is necessary for the control of the pandemic. Here, we give a systematic summary of the structures, immunoregulation, and potential vaccines and targeted drugs of the HCoVs N protein. First, we provide a general introduction to the fundamental structures and molecular function of N protein. Next, we outline the N protein mediated immune regulation and pathogenesis mechanism. Finally, we comprehensively summarize the development of potential N protein-targeted drugs and candidate vaccines to treat coronavirus disease 2019 (COVID-19). We believe this review provides insight into the virulence and transmission of SARS-CoV-2 as well as support for further study on epidemic control of COVID-19.
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Affiliation(s)
- Bo Zhang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
- *Correspondence: Yang Liu, ; Keyu Lu, ; Bo Zhang,
| | - Junjie Tian
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Qintao Zhang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Yan Xie
- School of Public Health, Zunyi Medical University, Zunyi, China
| | - Kejia Wang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Shuyi Qiu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Keyu Lu
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
- *Correspondence: Yang Liu, ; Keyu Lu, ; Bo Zhang,
| | - Yang Liu
- School of Public Health, Zunyi Medical University, Zunyi, China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- *Correspondence: Yang Liu, ; Keyu Lu, ; Bo Zhang,
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Zhou D, Wang EW, Hou C, Liao J, Zhang J, Fu X, Chen J, Xing Y, Hong W, Zhang Z, Chen Y, Feng H, Chen Y, Yang Q, Zhang H, Li Z, Feng W, Wang T, Lin Z, Zhang C, Yang K, Lu W, Wang J, Chen Y. Visibility, Wind speed, and Dew point temperature are important factors in SARS‐CoV‐2 transmissibility. Pulm Circ 2022; 12:e12081. [PMID: 35514785 PMCID: PMC9063952 DOI: 10.1002/pul2.12081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/25/2022] [Accepted: 04/06/2022] [Indexed: 11/09/2022] Open
Abstract
The aim of this study is to provide evidence for the influencing factors of severe acute respiratory syndrome coronavirus 2 (SARS‐COV‐2) virus mutation by determining the impact of geographical and meteorological factors on SARS‐CoV‐2 transmission, and the different impacts of SARS‐CoV‐2 variant strains. From January 20 to March 10, 2020, we collected a number of daily confirmed new cases and meteorological factors in all cities and regions in China and Italy affected by the Alpha “variants of concern” (VOC). We also collected the daily confirmed cases of the Delta VOC infection in China and Italy from May 21 to November 30, 2021. The relationships between daily meteorological data and daily verified new cases of SARS‐CoV‐2 transmission were then investigated using a general additive model (GAM) with a log link function and Poisson family. The results revealed that latitude was substantially connected with daily confirmed new instances of the Alpha VOC, while there was no such correlation with Delta VOC transmission. When visibility is greater than 7 m, the propagation of the Alpha and Delta VOCs in Italy and China can be controlled. Furthermore, greater temperatures and increased wind speed reduce the transmission of the Alpha and Delta VOCs. In conclusion, geographical and meteorological factors play an important role in SARS‐CoV‐2 transmissibility and should be considered in virus mitigation strategies.
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Affiliation(s)
- Dansha Zhou
- State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangdong‐Hong Kong‐Macao Joint Laboratory of Respiratory Infectious Disease Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University Guangzhou 510000 China
| | - Elizabeth Wenqian Wang
- Department of Infectious Diseases University of Maryland St. Joseph Medical Center Towson Maryland USA
| | - Chi Hou
- State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangdong‐Hong Kong‐Macao Joint Laboratory of Respiratory Infectious Disease Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University Guangzhou 510000 China
- Department of Neurology, Guangzhou Women and Children's Medical Center Guangzhou 510000 China
| | - Jing Liao
- School of Medicine Southern University of Science and Technology Shenzhen 518055 China
| | - Jiarui Zhang
- State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangdong‐Hong Kong‐Macao Joint Laboratory of Respiratory Infectious Disease Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University Guangzhou 510000 China
| | - Xin Fu
- GMU‐GIBH Joint School of Life Sciences Guangzhou Medical University, Guangzhou Guangdong China
| | - Jiyuan Chen
- State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangdong‐Hong Kong‐Macao Joint Laboratory of Respiratory Infectious Disease Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University Guangzhou 510000 China
| | - Yue Xing
- State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangdong‐Hong Kong‐Macao Joint Laboratory of Respiratory Infectious Disease Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University Guangzhou 510000 China
| | - Wei Hong
- GMU‐GIBH Joint School of Life Sciences Guangzhou Medical University, Guangzhou Guangdong China
| | - Zhe Zhang
- State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangdong‐Hong Kong‐Macao Joint Laboratory of Respiratory Infectious Disease Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University Guangzhou 510000 China
| | - Yuanwei Chen
- State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangdong‐Hong Kong‐Macao Joint Laboratory of Respiratory Infectious Disease Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University Guangzhou 510000 China
| | - Huazhuo Feng
- State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangdong‐Hong Kong‐Macao Joint Laboratory of Respiratory Infectious Disease Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University Guangzhou 510000 China
| | - Yilin Chen
- State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangdong‐Hong Kong‐Macao Joint Laboratory of Respiratory Infectious Disease Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University Guangzhou 510000 China
| | - Qifeng Yang
- State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangdong‐Hong Kong‐Macao Joint Laboratory of Respiratory Infectious Disease Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University Guangzhou 510000 China
| | - Huosheng Zhang
- State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangdong‐Hong Kong‐Macao Joint Laboratory of Respiratory Infectious Disease Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University Guangzhou 510000 China
| | - Zicong Li
- State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangdong‐Hong Kong‐Macao Joint Laboratory of Respiratory Infectious Disease Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University Guangzhou 510000 China
| | - Weici Feng
- State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangdong‐Hong Kong‐Macao Joint Laboratory of Respiratory Infectious Disease Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University Guangzhou 510000 China
| | - Ting Wang
- Department of Respiratory Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders Ministry of Education Key Laboratory of Child Development and Disorders Chongqing China
| | - Ziying Lin
- State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangdong‐Hong Kong‐Macao Joint Laboratory of Respiratory Infectious Disease Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University Guangzhou 510000 China
| | - Chenting Zhang
- State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangdong‐Hong Kong‐Macao Joint Laboratory of Respiratory Infectious Disease Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University Guangzhou 510000 China
| | - Kai Yang
- State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangdong‐Hong Kong‐Macao Joint Laboratory of Respiratory Infectious Disease Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University Guangzhou 510000 China
| | - Wenju Lu
- State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangdong‐Hong Kong‐Macao Joint Laboratory of Respiratory Infectious Disease Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University Guangzhou 510000 China
| | - Jian Wang
- State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangdong‐Hong Kong‐Macao Joint Laboratory of Respiratory Infectious Disease Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University Guangzhou 510000 China
| | - Yuqin Chen
- State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangdong‐Hong Kong‐Macao Joint Laboratory of Respiratory Infectious Disease Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University Guangzhou 510000 China
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Yang Z, Zhang S, Tang YP, Zhang S, Xu DQ, Yue SJ, Liu QL. Clinical Characteristics, Transmissibility, Pathogenicity, Susceptible Populations, and Re-infectivity of Prominent COVID-19 Variants. Aging Dis 2022; 13:402-422. [PMID: 35371608 PMCID: PMC8947836 DOI: 10.14336/ad.2021.1210] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/10/2021] [Indexed: 12/11/2022] Open
Abstract
In addition to the rapid, global spread of SARS-CoV-2, new and comparatively more contagious variants are of considerable concern. These emerging mutations have become a threat to the global public health, creating COVID-19 surges in different countries. However, information on these emerging variants is limited and scattered. In this review, we discuss new variants that have emerged worldwide and identify several variants of concern, such as B.1.1.7, B.1.351, P.1, B.1.617.2 and B.1.1.529, and their basic characteristics. Other significant variants such as C.37, B.1.621, B.1.525, B.1.526, AZ.5, C.1.2, and B.1.617.1 are also discussed. This review highlights the clinical characteristics of these variants, including transmissibility, pathogenicity, susceptible population, and re-infectivity. It provides the latest information on the recent variants of SARS-CoV-2. The summary of this information will help researchers formulate reasonable strategies to curb the ongoing COVID-19 pandemic.
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Affiliation(s)
- Zhen Yang
- 1Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China.,2School of Public Health, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China
| | - Shuo Zhang
- 3School of Clinical Medicine (Guang'anmen Hospital), Beijing University of Chinese Medicine, Beijing, China
| | - Yu-Ping Tang
- 1Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China
| | - Sai Zhang
- 1Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China
| | - Ding-Qiao Xu
- 1Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China
| | - Shi-Jun Yue
- 1Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China
| | - Qi-Ling Liu
- 2School of Public Health, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China
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Wang CY, Hwang KP, Kuo HK, Peng WJ, Shen YH, Kuo BS, Huang JH, Liu H, Ho YH, Lin F, Ding S, Liu Z, Wu HT, Huang CT, Lee YJ, Liu MC, Yang YC, Lu PL, Tsai HC, Lee CH, Shi ZY, Liu CE, Liao CH, Chang FY, Cheng HC, Wang FD, Hou KL, Cheng J, Wang MS, Yang YT, Chiu HC, Jiang MH, Shih HY, Shen HY, Chang PY, Lan YR, Chen CT, Lin YL, Liang JJ, Liao CC, Chou YC, Morris MK, Hanson CV, Guirakhoo F, Hellerstein M, Yu HJ, King CC, Kemp T, Heppner DG, Monath TP. A multitope SARS-COV-2 vaccine provides long-lasting B cell and T cell immunity against Delta and Omicron variants. J Clin Invest 2022; 132:157707. [PMID: 35316221 PMCID: PMC9106357 DOI: 10.1172/jci157707] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/16/2022] [Indexed: 11/19/2022] Open
Abstract
Background The Delta and Omicron variants of SARS-CoV-2 are currently responsible for breakthrough infections due to waning immunity. We report phase I/II trial results of UB-612, a multitope subunit vaccine containing S1-RBD-sFc protein and rationally designed promiscuous peptides representing sarbecovirus conserved helper T cell and cytotoxic T lymphocyte epitopes on the nucleocapsid (N), membrane (M), and spike (S2) proteins. Method We conducted a phase I primary 2-dose (28 days apart) trial of 10, 30, or 100 μg UB-612 in 60 healthy young adults 20 to 55 years old, and 50 of them were boosted with 100 μg of UB-612 approximately 7 to 9 months after the second dose. A separate placebo-controlled and randomized phase II study was conducted with 2 doses of 100 μg of UB-612 (n = 3,875, 18–85 years old). We evaluated interim safety and immunogenicity of phase I until 14 days after the third (booster) dose and of phase II until 28 days after the second dose. Results No vaccine-related serious adverse events were recorded. The most common solicited adverse events were injection site pain and fatigue, mostly mild and transient. In both trials, UB-612 elicited respective neutralizing antibody titers similar to a panel of human convalescent sera. The most striking findings were long-lasting virus-neutralizing antibodies and broad T cell immunity against SARS-CoV-2 variants of concern (VoCs), including Delta and Omicron, and a strong booster-recalled memory immunity with high cross-reactive neutralizing titers against the Delta and Omicron VoCs. Conclusion UB-612 has presented a favorable safety profile, potent booster effect against VoCs, and long-lasting B and broad T cell immunity that warrants further development for both primary immunization and heterologous boosting of other COVID-19 vaccines. Trial Registration ClinicalTrials.gov: NCT04545749, NCT04773067, and NCT04967742. Funding UBI Asia, Vaxxinity Inc., and Taiwan Centers for Disease Control, Ministry of Health and Welfare.
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Affiliation(s)
| | - Kao-Pin Hwang
- Division of Infectious Diseases, China Medical University Children's Hospital, Taichung City, Taiwan
| | - Hui-Kai Kuo
- Designed Vaccine Translation Medical Center, UBI Asia, Hsinchu, Taiwan
| | - Wen-Jiun Peng
- Administrative Management Center, UBI Asia, Hsinchu, Taiwan
| | - Yea-Huei Shen
- Medical and Clinical Operation, StatPlus, Taipei, Taiwan
| | - Be-Sheng Kuo
- Preclinical and ImmunoPharmacology Center, UBI Asia, Hsinchu, Taiwan
| | | | | | - Yu-Hsin Ho
- Regulatory Affairs, UBI Asia, Hsinchu, Taiwan
| | - Feng Lin
- R&D Center, United Bioimedical, Inc., Hauppauge, United States of America
| | - Shuang Ding
- R&D Center, United Biomedical, Inc., Hauppauge, United States of America
| | - Zhi Liu
- R&D Center, United Biomedical, Inc., Hauppauge, United States of America
| | | | - Ching-Tai Huang
- Department of Infectious Disease, Chang Gung University, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Yuarn-Jang Lee
- Division of Infectious Diseases, Taipei Medical University Hospital, Taipei, Taiwan
| | - Ming-Che Liu
- R&D, Taipei Medical University Hospital, Taipei, Taiwan
| | - Yi-Ching Yang
- Ministry of Health and Welfare, National Cheng Kung University and Hospital, Tainan, Taiwan
| | - Po-Liang Lu
- Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Hung-Chin Tsai
- School of Medicine, Kaohsiung Veterans General Hospital, Kaoshiung, Taiwan
| | - Chen-Hsiang Lee
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Zhi-Yuan Shi
- Department of Medical Affairs, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chun-Eng Liu
- Department of Medical Affairs, Changhua Christian Hospital, Changhua, Taiwan
| | - Chun-Hsing Liao
- Department of Medical Affairs, Far Eastern Memorial Hospital, New Taipei, Taiwan
| | - Feng-Yee Chang
- Department of Internal Medicine, Tri-Service General Hospital, Taipei, Taiwan
| | - Hsiang-Cheng Cheng
- Department of Medical Affairs, Tri-Service General Hospital, Taipei, Taiwan
| | - Fu-Der Wang
- Department of Internal Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Kuo-Liang Hou
- Department of Preclinical Research, UBI Asia, Hsinchu, Taiwan
| | - Jennifer Cheng
- Department of Preclinical Research, UBI Asia, Hsinchu, Taiwan
| | - Min-Sheng Wang
- Department of Clinical Research, UBI Asia, Hsinchu, Taiwan
| | - Ya-Ting Yang
- Department of Preclinical Research, UBI Asia, Hsinchu, Taiwan
| | - Han-Chen Chiu
- Department of Medical Affairs, UBI Asia, Hsinchu, Taiwan
| | - Ming-Han Jiang
- Department of Preclinical Research, UBI Asia, Hsinchu, Taiwan
| | - Hao-Yu Shih
- Department of Preclinical Research, UBI Asia, Hsinchu, Taiwan
| | - Hsuan-Yu Shen
- Department of Clinical Research, UBI Asia, Hsinchu, Taiwan
| | - Po-Yen Chang
- Department of Clinical Research, UBI Asia, Hsinchu, Taiwan
| | - Yu-Rou Lan
- Department of Preclinical Research, UBI Asia, Hsinchu, Taiwan
| | - Chi-Tian Chen
- Biostatistics and Data Management, StatPlus, Taipei, Taiwan
| | - Yi-Ling Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jian-Jong Liang
- Biomedical Translation Research Center (bioTReC) Academia Sinica, Taipei, Taiwan
| | - Chun-Che Liao
- Department of Medical Affairs, Biomedical Translation Research Center (bioTReC) Academia Sinica, Taipei, Taiwan
| | - Yu-Chi Chou
- Department of Statistics, Biomedical Translation Research Center (bioTReC) Academia Sinica, Taipei, Taiwan
| | - Mary Kate Morris
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, United States of America
| | - Carl V Hanson
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, United States of America
| | - Farshad Guirakhoo
- Department of Clinical Research, Vaxxinity Inc., Dallas, United States of America
| | - Michael Hellerstein
- Department of Preclinical Research, Vaxxinity Inc., Dallas, United States of America
| | - Hui Jing Yu
- Department of Clinical Research, Vaxxinity Inc., Dallas, United States of America
| | - Chwan-Chuen King
- Department of Medical, Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Tracy Kemp
- Department of Clinical Research, Vaxxinity, Inc., Dallas, United States of America
| | - D Gray Heppner
- Department of Clinical Research, Vaxxinity, Inc., Dallas, United States of America
| | - Thomas P Monath
- Department of Clinical Research, Vaxxinity, Inc., Dallas, United States of America
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Murae M, Shimizu Y, Yamamoto Y, Kobayashi A, Houri M, Inoue T, Irie T, Gemba R, Kondo Y, Nakano Y, Miyazaki S, Yamada D, Saitoh A, Ishii I, Onodera T, Takahashi Y, Wakita T, Fukasawa M, Noguchi K. The function of SARS-CoV-2 spike protein is impaired by disulfide-bond disruption with mutation at cysteine-488 and by thiol-reactive N-acetyl-cysteine and glutathione. Biochem Biophys Res Commun 2022; 597:30-36. [PMID: 35123263 PMCID: PMC8800159 DOI: 10.1016/j.bbrc.2022.01.106] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 01/26/2022] [Indexed: 12/12/2022]
Abstract
Viral spike proteins play important roles in the viral entry process, facilitating attachment to cellular receptors and fusion of the viral envelope with the cell membrane. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein binds to the cellular receptor angiotensin converting enzyme-2 (ACE2) via its receptor-binding domain (RBD). The cysteine residue at position 488, consisting of a disulfide bridge with cysteine 480 is located in an important structural loop at ACE2-binding surface of RBD, and is highly conserved among SARS-related coronaviruses. We showed that the substitution of Cys-488 with alanine impaired pseudotyped SARS-CoV-2 infection, syncytium formation, and cell-cell fusion triggered by SARS-CoV-2 spike expression. Consistently, in vitro binding of RBD and ACE2, spike-mediated cell-cell fusion, and pseudotyped viral infection of VeroE6/TMPRSS2 cells were inhibited by the thiol-reactive compounds N-acetylcysteine (NAC) and a reduced form of glutathione (GSH). Furthermore, we demonstrated that the activity of variant spikes from the SARS-CoV-2 alpha and delta strains were also suppressed by NAC and GSH. Taken together, these data indicate that Cys-488 in spike RBD is required for SARS-CoV-2 spike functions and infectivity, and could be a target of anti-SARS-CoV-2 therapeutics.
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Affiliation(s)
- Mana Murae
- Laboratory of Molecular Target Therapy, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamasaki 2641, Noda, Chiba, 278-8510, Japan; Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Yoshimi Shimizu
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan; Department of Pharmaceutical Sciences, Teikyo Heisei University, 4-21-2 Nakano, Nakano-ku, 164-8530, Japan
| | - Yuichiro Yamamoto
- Laboratory of Molecular Target Therapy, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamasaki 2641, Noda, Chiba, 278-8510, Japan
| | - Asuka Kobayashi
- Laboratory of Molecular Target Therapy, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamasaki 2641, Noda, Chiba, 278-8510, Japan
| | - Masumi Houri
- Laboratory of Molecular Target Therapy, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamasaki 2641, Noda, Chiba, 278-8510, Japan
| | - Tetsuya Inoue
- Laboratory of Molecular Target Therapy, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamasaki 2641, Noda, Chiba, 278-8510, Japan
| | - Takuya Irie
- Laboratory of Molecular Target Therapy, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamasaki 2641, Noda, Chiba, 278-8510, Japan; Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Ryutaro Gemba
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Yosuke Kondo
- Department of Medical and Life Science, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamasaki 2641, Noda, Chiba, 278-8510, Japan
| | - Yoshio Nakano
- Department of Medical and Life Science, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamasaki 2641, Noda, Chiba, 278-8510, Japan
| | - Satoru Miyazaki
- Department of Medical and Life Science, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamasaki 2641, Noda, Chiba, 278-8510, Japan
| | - Daisuke Yamada
- Laboratory of Pharmacology, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamasaki 2641, Noda, Chiba, 278-8510, Japan
| | - Akiyoshi Saitoh
- Laboratory of Pharmacology, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamasaki 2641, Noda, Chiba, 278-8510, Japan
| | - Isao Ishii
- Department of Health Chemistry, Showa Pharmaceutical University, Tokyo, 194-8543, Japan
| | - Taishi Onodera
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Yoshimasa Takahashi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Takaji Wakita
- National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Masayoshi Fukasawa
- Laboratory of Molecular Target Therapy, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamasaki 2641, Noda, Chiba, 278-8510, Japan; Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan.
| | - Kohji Noguchi
- Laboratory of Molecular Target Therapy, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamasaki 2641, Noda, Chiba, 278-8510, Japan; Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan.
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Biswas B, Chattopadhyay S, Hazra S, Hansda AK, Goswami R. COVID-19 pandemic: the delta variant, T-cell responses, and the efficacy of developing vaccines. Inflamm Res 2022; 71:377-396. [PMID: 35292834 PMCID: PMC8923340 DOI: 10.1007/s00011-022-01555-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/07/2022] [Accepted: 02/16/2022] [Indexed: 12/15/2022] Open
Abstract
Background The mayhem COVID-19 that was ushered by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) was declared pandemic by the World Health Organization in March 2020. Since its initial outbreak in late 2019, the virus has affected hundreds of million adults in the world and killing millions in the process. After the approval of newly developed vaccines, severe challenges remain to manufacture and administer them to the adult population globally in quick time. However, we have witnessed several mutations of the virus leading to ‘waves’ of viral spread and mortality. WHO has categorized these mutations as variants of concern (VOCs) and variants of interest (VOIs). The mortality due to COVID-19 has also been associated with various comorbidities and improper immune response. This has created further complications in understanding the nature of the SARS-CoV2–host interaction that has fuelled doubts in the efficacy of the approved vaccines. Whether there is requirement of booster dose and whether the impending wave could affect the children are some of the hotly debated topics. Materials and Methods A systematic literature review of PubMed, Medline, Scopus, Google Scholar was utilized to understand the nature of Delta variant and how it alters our T-cell responses and cytokine production and neutralizes vaccine-generated antibodies.
Conclusion In this review, we discuss the variants of SARS-CoV2 with specific focus on the Delta variant. We also specifically review the T-cell response against the virus and bring a narrative of various factors that may hold the key to fight against this marauding virus.
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Affiliation(s)
- Biswajit Biswas
- School of Bioscience, IIT Kharagpur, Kharagpur, 721302, West Bengal, India
| | | | - Sayantee Hazra
- School of Bioscience, IIT Kharagpur, Kharagpur, 721302, West Bengal, India
| | | | - Ritobrata Goswami
- School of Bioscience, IIT Kharagpur, Kharagpur, 721302, West Bengal, India.
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Jin Y, Hou C, Li Y, Zheng K, Wang C. mRNA Vaccine: How to Meet the Challenge of SARS-CoV-2. Front Immunol 2022; 12:821538. [PMID: 35126377 PMCID: PMC8813741 DOI: 10.3389/fimmu.2021.821538] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/27/2021] [Indexed: 12/13/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with high infectivity, pathogenicity, and variability, is a global pandemic that severely affected public health and the world economy. The development of safe and effective vaccines is crucial to the prevention and control of an epidemic. As an emerging technology, mRNA vaccine is widely used for infectious disease prevention and control and has significant safety, efficacy, and high production. It has received support and funding from many pharmaceutical enterprises and becomes one of the main technologies for preventing COVID-19. This review introduces the current status of SARS-CoV-2 vaccines, specifically mRNA vaccines, focusing on the challenges of developing mRNA vaccines against SARS-CoV-2, and discusses the relevant strategies.
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Affiliation(s)
- Yingqi Jin
- Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, China
| | - Chen Hou
- Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, China
| | - Yonghao Li
- Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, China
| | - Kang Zheng
- Department of Clinical Laboratory, Hengyang Central Hospital, Hengyang, China
| | - Chuan Wang
- Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, China
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
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Zhang M, Liang Y, Yu D, Du B, Cheng W, Li L, Yu Z, Luo S, Zhang Y, Wang H, Zhang X, Zhang W. A systematic review of Vaccine Breakthrough Infections by SARS-CoV-2 Delta Variant. Int J Biol Sci 2022; 18:889-900. [PMID: 35002532 PMCID: PMC8741840 DOI: 10.7150/ijbs.68973] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/02/2021] [Indexed: 12/11/2022] Open
Abstract
Vaccines are proving to be highly effective in controlling hospitalization and deaths associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, as shown by clinical trials and real-world evidence. However, a deadly second wave of coronavirus disease 2019 (COVID-19), infected by SARS-CoV-2 variants, especially the Delta (B.1.617.2) variant, with an increased number of post-vaccination breakthrough infections were reported in the world recently. Actually, Delta variant not only resulted in a severe surge of vaccine breakthrough infections which was accompanied with high viral load and transmissibility, but also challenged the development of effective vaccines. Therefore, the biological characteristics and epidemiological profile of Delta variant, the current status of Delta variant vaccine breakthrough infections and the mechanism of vaccine breakthrough infections were discussed in this article. In addition, the significant role of the Delta variant spike (S) protein in the mechanism of immune escape of SARS-CoV-2 was highlighted in this article. In particular, we further discussed key points on the future SARS-CoV-2 vaccine research and development, hoping to make a contribution to the early, accurate and rapid control of the COVID-19 epidemic.
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Affiliation(s)
- Mengxin Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Ying Liang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Dongsheng Yu
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, China
| | - Bang Du
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Weyland Cheng
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Lifeng Li
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Zhidan Yu
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Shuying Luo
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Yaodong Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Huanmin Wang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Xianwei Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Wancun Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
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In Silico Screening of Potential Phytocompounds from Several Herbs against SARS-CoV-2 Indian Delta Variant B.1.617.2 to Inhibit the Spike Glycoprotein Trimer. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12020665] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In October 2020, the SARS-CoV-2 B.1.617 lineage was discovered in India. It has since become a prominent variant in several Indian regions and 156 countries, including the United States of America. The lineage B.1.617.2 is termed the delta variant, harboring diverse spike mutations in the N-terminal domain (NTD) and the receptor-binding domain (RBD), which may heighten its immune evasion potentiality and cause it to be more transmissible than other variants. As a result, it has sparked substantial scientific investigation into the development of effective vaccinations and anti-viral drugs. Several efforts have been made to examine ancient medicinal herbs known for their health benefits and immune-boosting action against SARS-CoV-2, including repurposing existing FDA-approved anti-viral drugs. No efficient anti-viral drugs are available against the SARS-CoV-2 Indian delta variant B.1.617.2. In this study, efforts were made to shed light on the potential of 603 phytocompounds from 22 plant species to inhibit the Indian delta variant B.1.617.2. We also compared these compounds with the standard drug ceftriaxone, which was already suggested as a beneficial drug in COVID-19 treatment; these compounds were compared with other FDA-approved drugs: remdesivir, chloroquine, hydroxy-chloroquine, lopinavir, and ritonavir. From the analysis, the identified phytocompounds acteoside (−7.3 kcal/mol) and verbascoside (−7.1 kcal/mol), from the plants Clerodendrum serratum and Houttuynia cordata, evidenced a strong inhibitory effect against the mutated NTD (MT-NTD). In addition, the phytocompounds kanzonol V (−6.8 kcal/mol), progeldanamycin (−6.4 kcal/mol), and rhodoxanthin (−7.5 kcal/mol), from the plant Houttuynia cordata, manifested significant prohibition against RBD. Nevertheless, the standard drug, ceftriaxone, signals less inhibitory effect against MT-NTD and RBD with binding affinities of −6.3 kcal/mol and −6.5 kcal/mol, respectively. In this study, we also emphasized the pharmacological properties of the plants, which contain the screened phytocompounds. Our research could be used as a lead for future drug design to develop anti-viral drugs, as well as for preening the Siddha formulation to control the Indian delta variant B.1.617.2 and other future SARS-CoV-2 variants.
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Hossen ML, Baral P, Sharma T, Gerstman BS, Chapagain P. Significance of the RBD mutations in the SARS-CoV-2 Omicron: from spike opening to antibody escape and cell attachment. Phys Chem Chem Phys 2022; 24:9123-9129. [DOI: 10.1039/d2cp00169a] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We computationally investigated the role of the Omicron RBD mutations on its structure and interactions with surrounding domains in the spike trimer as well as with ACE2. Our results suggest...
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49
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Li G, Zhang L, Xue P. Codon usage divergence in Delta variants (B.1.617.2) of SARS-CoV-2. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 97:105175. [PMID: 34871776 PMCID: PMC8641433 DOI: 10.1016/j.meegid.2021.105175] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/27/2021] [Accepted: 12/01/2021] [Indexed: 01/17/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spreads all over the world and brings great harm to humans in many countries. Many new SARS-CoV-2 variants appeared during its transmission. In the present study, the Delta variants (B.1.617.2) of SARS-CoV-2, which have appeared in many countries, were considered for analysis. In order to evaluate the evolutionary divergence of the Delta variants(B.1.617.2), the codon usage divergence in Delta variants (B.1.617.2) of SARS-CoV-2 was compared to that of the SARS-CoV-2 genomes emerged before June 2020. All Delta variants (B.1.617.2) and 350 early genomes of SARS-CoV-2 in the NCBI database were downloaded. Codon usage pattern including the basic composition, the GC ratio of the third position (GC3) and the first two positions (GC12) in codons, overall GC contents, the effective number of codons (ENC), the codon bias index (CBI), the relative synonymous codon usage (RSCU) values, etc., of all concerned important gene sequences were all calculated. Codon usage divergence of them was calculated via summing their standard deviations. The results suggested that base compositions in both Delta variants (B.1.617.2) of SARS-CoV-2 and the early SARS-CoV-2 genomes were similar to each other. However, the internal codon usage divergence for most genes in Delta variants (B.1.617.2) was significantly wider than that of SARS-CoV-2. The RSCU values were further used to explore the synonymous and non-synonymous mutations in the sequences of the Delta variants (B.1.617.2), and the results showed the synonymous mutations are more obvious than the non-synonymous in the concerned sequences. The related codon usage divergence analysis is helpful for further study on the adaptability and disease prognosis of the SARS-CoV-2 variants.
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Affiliation(s)
- Gun Li
- Laboratory for Biodiversity Science, Department of Biomedical Engineering, School of Electronic Information Engineering, Xi'An Technological University, Xi'An, China.
| | - Liang Zhang
- Laboratory for Biodiversity Science, Department of Biomedical Engineering, School of Electronic Information Engineering, Xi'An Technological University, Xi'An, China
| | - Pei Xue
- Laboratory for Biodiversity Science, Department of Biomedical Engineering, School of Electronic Information Engineering, Xi'An Technological University, Xi'An, China
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Valério M, Borges-Araújo L, Melo MN, Lousa D, Soares CM. SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility. FRONTIERS IN MEDICAL TECHNOLOGY 2022; 4:1009451. [PMID: 36277437 PMCID: PMC9581196 DOI: 10.3389/fmedt.2022.1009451] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/20/2022] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed over 6 million people and is having a devastating social and economic impact around the world. The rise of new variants of concern (VOCs) represents a difficult challenge due to the loss of vaccine and natural immunity, as well as increased transmissibility. All VOCs contain mutations in the spike glycoprotein, which mediates fusion between the viral and host cell membranes. The spike glycoprotein binds to angiotensin-converting enzyme 2 (ACE2) via its receptor binding domain (RBD) initiating the infection process. Attempting to understand the effect of RBD mutations in VOCs, a lot of attention has been given to the RBD-ACE2 interaction. However, this type of analysis ignores more indirect effects, such as the conformational dynamics of the RBD itself. Observing that some mutations occur in residues that are not in direct contact with ACE2, we hypothesized that they could affect the RBD conformational dynamics. To test this, we performed long atomistic (AA) molecular dynamics (MD) simulations to investigate the structural dynamics of wt RBD, and that of four VOCs (Alpha, Beta, Delta, and Omicron). Our results show that the wt RBD presents two distinct conformations: an "open" conformation where it is free to bind ACE2; and a "closed" conformation, where the RBM ridge blocks the binding surface. The Alpha and Beta variants shift the open/closed equilibrium towards the open conformation by roughly 20%, likely increasing ACE2 binding affinity. Simulations of the Delta and Omicron variants showed extreme results, with the closed conformation being rarely observed. The Delta variant also differed substantially from the other variants, alternating between the open conformation and an alternative "reversed" one, with a significantly changed orientation of the RBM ridge. This alternate conformation could provide a fitness advantage due to increased availability for ACE2 binding, and by aiding antibody escape through epitope occlusion. These results support the hypothesis that VOCs, and particularly the Omicron and Delta variants, impact RBD conformational dynamics in a direction that promotes efficient binding to ACE2 and, in the case of Delta, may assist antibody escape.
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Affiliation(s)
- Mariana Valério
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Luís Borges-Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
- Correspondence: Manuel N. Melo Diana Lousa Cláudio M. Soares
| | - Diana Lousa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
- Correspondence: Manuel N. Melo Diana Lousa Cláudio M. Soares
| | - Cláudio M. Soares
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
- Correspondence: Manuel N. Melo Diana Lousa Cláudio M. Soares
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