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For: Zhang J, Xiao T, Cai Y, Lavine CL, Peng H, Zhu H, Anand K, Tong P, Gautam A, Mayer ML, Walsh RM, Rits-Volloch S, Wesemann DR, Yang W, Seaman MS, Lu J, Chen B. Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant. Science 2021;374:1353-1360. [PMID: 34698504 PMCID: PMC10763652 DOI: 10.1126/science.abl9463] [Citation(s) in RCA: 212] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 10/22/2021] [Indexed: 12/15/2022]
Number Cited by Other Article(s)
51
Ramasamy R. Overview of immunological & virological factors driving the evolution & global spread of SARS-CoV-2 variants. Indian J Med Res 2023;158:257-268. [PMID: 37815068 PMCID: PMC10720969 DOI: 10.4103/ijmr.ijmr_2591_22] [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: 12/21/2022] [Indexed: 10/11/2023]  Open
52
Xiao S, Alshahrani M, Gupta G, Tao P, Verkhivker G. Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms. J Chem Inf Model 2023;63:5272-5296. [PMID: 37549201 PMCID: PMC11162552 DOI: 10.1021/acs.jcim.3c00778] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
53
Verkhivker G, Alshahrani M, Gupta G, Xiao S, Tao P. Probing conformational landscapes of binding and allostery in the SARS-CoV-2 omicron variant complexes using microsecond atomistic simulations and perturbation-based profiling approaches: hidden role of omicron mutations as modulators of allosteric signaling and epistatic relationships. Phys Chem Chem Phys 2023;25:21245-21266. [PMID: 37548589 PMCID: PMC10536792 DOI: 10.1039/d3cp02042h] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
54
Wang H, Yuan Y, Wu B, Xiao M, Wang Z, Diao T, Zeng R, Chen L, Lei Y, Long P, Guo Y, Lai X, Wen Y, Li W, Cai H, Song L, Ni W, Zhao Y, Ouyang K, Wang J, Wang Q, Liu L, Wang C, Pan A, Li X, Gong R, Wu T. Neutralization against SARS-CoV-2 Delta/Omicron variants and B cell response after inactivated vaccination among COVID-19 convalescents. Front Med 2023;17:747-757. [PMID: 36738428 PMCID: PMC9898702 DOI: 10.1007/s11684-022-0954-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/20/2022] [Indexed: 02/05/2023]
55
Sergeeva AP, Katsamba PS, Liao J, Sampson JM, Bahna F, Mannepalli S, Morano NC, Shapiro L, Friesner RA, Honig B. Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity. J Mol Biol 2023;435:168187. [PMID: 37355034 PMCID: PMC10286572 DOI: 10.1016/j.jmb.2023.168187] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/26/2023]
56
Dokainish HM, Sugita Y. Structural effects of spike protein D614G mutation in SARS-CoV-2. Biophys J 2023;122:2910-2920. [PMID: 36397671 PMCID: PMC9671695 DOI: 10.1016/j.bpj.2022.11.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 09/02/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]  Open
57
Reuter N, Chen X, Kropff B, Peter AS, Britt WJ, Mach M, Überla K, Thomas M. SARS-CoV-2 Spike Protein Is Capable of Inducing Cell-Cell Fusions Independent from Its Receptor ACE2 and This Activity Can Be Impaired by Furin Inhibitors or a Subset of Monoclonal Antibodies. Viruses 2023;15:1500. [PMID: 37515187 PMCID: PMC10384293 DOI: 10.3390/v15071500] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023]  Open
58
Zhang J, Tang W, Gao H, Lavine CL, Shi W, Peng H, Zhu H, Anand K, Kosikova M, Kwon HJ, Tong P, Gautam A, Rits-Volloch S, Wang S, Mayer ML, Wesemann DR, Seaman MS, Lu J, Xiao T, Xie H, Chen B. Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein. Nat Struct Mol Biol 2023;30:980-990. [PMID: 37430064 DOI: 10.1038/s41594-023-01023-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/17/2023] [Indexed: 07/12/2023]
59
Wu CY, Yang YH, Lin YS, Shu LH, Cheng YC, Liu HT, Lin YY, Lee IY, Shih WT, Yang PR, Tsai YY, Chang GH, Hsu CM, Yeh RA, Wu YH, Wu YH, Shen RC, Tsai MS. The anti-SARS-CoV-2 effect and mechanism of Chiehyuan herbal oral protection solution. Heliyon 2023;9:e17701. [PMID: 37483781 PMCID: PMC10359827 DOI: 10.1016/j.heliyon.2023.e17701] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 06/07/2023] [Accepted: 06/26/2023] [Indexed: 07/25/2023]  Open
60
Giron CC, Laaksonen A, Barroso da Silva FL. Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies. J Biomol Struct Dyn 2023;41:5707-5727. [PMID: 35815535 DOI: 10.1080/07391102.2022.2095305] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/23/2022] [Indexed: 12/23/2022]
61
Hu S, Wang N, Chen S, Zhang H, Wang C, Ma W, Zhang X, Wu Y, Lv Y, Xue Z, Bai H, Ge S, He H, Lu W, Zhang T, Ding Y, Liu R, Han S, Zhan Y, Zhan G, Guo Z, Zhang Y, Lu J, Gao J, Jia Q, Wang Y, Wang H, Lu S, Jin T, Chiu S, He L. Harringtonine: A more effective antagonist for Omicron variant. Biochem Pharmacol 2023;213:115617. [PMID: 37211174 PMCID: PMC10195862 DOI: 10.1016/j.bcp.2023.115617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/23/2023]
62
Gao J, Cao C, Shi M, Hong S, Guo S, Li J, Liang T, Song P, Xu R, Li N. Kaempferol inhibits SARS-CoV-2 invasion by impairing heptad repeats-mediated viral fusion. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023;118:154942. [PMID: 37421767 PMCID: PMC10289257 DOI: 10.1016/j.phymed.2023.154942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/17/2023] [Accepted: 06/22/2023] [Indexed: 07/10/2023]
63
Kuzmina A, Korovin D, Cohen Lass I, Atari N, Ottolenghi A, Hu P, Mandelboim M, Rosental B, Rosenberg E, Diaz-Griffero F, Taube R. Changes within the P681 residue of spike dictate cell fusion and syncytia formation of Delta and Omicron variants of SARS-CoV-2 with no effects on neutralization or infectivity. Heliyon 2023;9:e16750. [PMID: 37292300 PMCID: PMC10238279 DOI: 10.1016/j.heliyon.2023.e16750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 04/13/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023]  Open
64
Haddrell A, Otero-Fernandez M, Oswin H, Cogan T, Bazire J, Tian J, Alexander R, Mann JFS, Hill D, Finn A, Davidson AD, Reid JP. Differences in airborne stability of SARS-CoV-2 variants of concern is impacted by alkalinity of surrogates of respiratory aerosol. J R Soc Interface 2023;20:20230062. [PMID: 37340783 PMCID: PMC10282576 DOI: 10.1098/rsif.2023.0062] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/30/2023] [Indexed: 06/22/2023]  Open
65
Yi Y, Li W, Liu K, Xue H, Yu R, Zhang M, Bao YO, Lai X, Fan J, Huang Y, Wang J, Shi X, Li J, Wei H, Xiang K, Li L, Zhang R, Zhao X, Qiao X, Yang H, Ye M. Licorice-saponin A3 is a broad-spectrum inhibitor for COVID-19 by targeting viral spike and anti-inflammation. J Pharm Anal 2023:S2095-1779(23)00099-0. [PMID: 37363744 PMCID: PMC10201890 DOI: 10.1016/j.jpha.2023.05.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 06/28/2023]  Open
66
Xiao S, Alshahrani M, Gupta G, Tao P, Verkhivker G. Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variants Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.20.541592. [PMID: 37292827 PMCID: PMC10245745 DOI: 10.1101/2023.05.20.541592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
67
Verkhivker G, Alshahrani M, Gupta G. Balancing Functional Tradeoffs between Protein Stability and ACE2 Binding in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB Lineages: Dynamics-Based Network Models Reveal Epistatic Effects Modulating Compensatory Dynamic and Energetic Changes. Viruses 2023;15:1143. [PMID: 37243229 PMCID: PMC10221141 DOI: 10.3390/v15051143] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/27/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023]  Open
68
Verkhivker G, Alshahrani M, Gupta G, Xiao S, Tao P. Probing Conformational Landscapes of Binding and Allostery in the SARS-CoV-2 Omicron Variant Complexes Using Microsecond Atomistic Simulations and Perturbation-Based Profiling Approaches: Hidden Role of Omicron Mutations as Modulators of Allosteric Signaling and Epistatic Relationships. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539337. [PMID: 37205479 PMCID: PMC10187228 DOI: 10.1101/2023.05.03.539337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
69
Yurkovetskiy L, Egri S, Kurhade C, Diaz-Salinas MA, Jaimes JA, Nyalile T, Xie X, Choudhary MC, Dauphin A, Li JZ, Munro JB, Shi PY, Shen K, Luban J. S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.30.535005. [PMID: 37034621 PMCID: PMC10081308 DOI: 10.1101/2023.03.30.535005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
70
Deng S, Liu Y, Tam RCY, Chen P, Zhang AJ, Mok BWY, Long T, Kukic A, Zhou R, Xu H, Song W, Chan JFW, To KKW, Chen Z, Yuen KY, Wang P, Chen H. An intranasal influenza virus-vectored vaccine prevents SARS-CoV-2 replication in respiratory tissues of mice and hamsters. Nat Commun 2023;14:2081. [PMID: 37045873 PMCID: PMC10092940 DOI: 10.1038/s41467-023-37697-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/23/2023] [Indexed: 04/14/2023]  Open
71
Gili R, Burioni R. SARS-CoV-2 before and after Omicron: two different viruses and two different diseases? J Transl Med 2023;21:251. [PMID: 37038133 PMCID: PMC10088248 DOI: 10.1186/s12967-023-04095-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 03/28/2023] [Indexed: 04/12/2023]  Open
72
Furusawa Y, Kiso M, Iida S, Uraki R, Hirata Y, Imai M, Suzuki T, Yamayoshi S, Kawaoka Y. In SARS-CoV-2 delta variants, Spike-P681R and D950N promote membrane fusion, Spike-P681R enhances spike cleavage, but neither substitution affects pathogenicity in hamsters. EBioMedicine 2023;91:104561. [PMID: 37043872 PMCID: PMC10083686 DOI: 10.1016/j.ebiom.2023.104561] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/18/2023] [Accepted: 03/28/2023] [Indexed: 04/14/2023]  Open
73
Dual mechanism: Epigenetic inhibitor apabetalone reduces SARS-CoV-2 Delta and Omicron variant spike binding and attenuates SARS-CoV-2 RNA induced inflammation. Int Immunopharmacol 2023;117:109929. [PMID: 36857935 PMCID: PMC9946890 DOI: 10.1016/j.intimp.2023.109929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/03/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023]
74
Haque S, Mathkor DM, Alkhanani MF, Bantun F, Momenah AM, Faidah H, Jalal NA, Kumar V. Comprehensive deep mutational scanning reveals the pH induced stability and binding differences between SARS-CoV-2 spike RBD and human ACE2. J Biomol Struct Dyn 2023;41:15207-15218. [PMID: 36995177 DOI: 10.1080/07391102.2023.2194007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/25/2023] [Indexed: 03/31/2023]
75
Zhang Q, Tang WC, Stancanelli E, Jung E, Syed Z, Pagadala V, Saidi L, Chen CZ, Gao P, Xu M, Pavlinov I, Li B, Huang W, Chen L, Liu J, Xie H, Zheng W, Ye Y. Heparan sulfate promotes ACE2 super-cluster assembly to enhance SARS-CoV-2-associated syncytium formation. RESEARCH SQUARE 2023:rs.3.rs-2693563. [PMID: 37034606 PMCID: PMC10081376 DOI: 10.21203/rs.3.rs-2693563/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
76
He X, He C, Hong W, Yang J, Wei X. Research progress in spike mutations of SARS-CoV-2 variants and vaccine development. Med Res Rev 2023. [PMID: 36929527 DOI: 10.1002/med.21941] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 09/27/2022] [Accepted: 02/26/2023] [Indexed: 03/18/2023]
77
Triveri A, Casali E, Frasnetti E, Doria F, Frigerio F, Cinquini F, Pavoni S, Moroni E, Marchetti F, Serapian SA, Colombo G. Conformational Behavior of SARS-Cov-2 Spike Protein Variants: Evolutionary Jumps in Sequence Reverberate in Structural Dynamic Differences. J Chem Theory Comput 2023;19:2120-2134. [PMID: 36926878 PMCID: PMC10029694 DOI: 10.1021/acs.jctc.3c00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
78
Calvaresi V, Wrobel AG, Toporowska J, Hammerschmid D, Doores KJ, Bradshaw RT, Parsons RB, Benton DJ, Roustan C, Reading E, Malim MH, Gamblin SJ, Politis A. Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein. Nat Commun 2023;14:1421. [PMID: 36918534 PMCID: PMC10013288 DOI: 10.1038/s41467-023-36745-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/15/2023] [Indexed: 03/15/2023]  Open
79
Ramos-Guzmán CA, Andjelkovic M, Zinovjev K, Ruiz-Pernía JJ, Tuñón I. The impact of SARS-CoV-2 3CL protease mutations on nirmatrelvir inhibitory efficiency. Computational insights into potential resistance mechanisms. Chem Sci 2023;14:2686-2697. [PMID: 36908962 PMCID: PMC9993853 DOI: 10.1039/d2sc06584c] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/13/2023] [Indexed: 02/16/2023]  Open
80
Zhu Y, Li M, Liu N, Wu T, Han X, Zhao G, He Y. Development of highly effective LCB1-based lipopeptides targeting the spike receptor-binding motif of SARS-CoV-2. Antiviral Res 2023;211:105541. [PMID: 36682464 PMCID: PMC9851916 DOI: 10.1016/j.antiviral.2023.105541] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/07/2023] [Accepted: 01/12/2023] [Indexed: 01/21/2023]
81
Beahm DR, Deng Y, DeAngelo TM, Sarpeshkar R. Drug Cocktail Formulation via Circuit Design. IEEE TRANSACTIONS ON MOLECULAR, BIOLOGICAL, AND MULTI-SCALE COMMUNICATIONS 2023;9:28-48. [PMID: 37397625 PMCID: PMC10312325 DOI: 10.1109/tmbmc.2023.3246928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
82
Kwon HJ, Zhang J, Kosikova M, Tang W, Ortega-Rodriguez U, Peng H, Meseda CA, Pedro CL, Schmeisser F, Lu J, Kang I, Zhou B, Davis CT, Wentworth DE, Chen WH, Shriver MC, Barnes RS, Pasetti MF, Weir JP, Chen B, Xie H. Distinct in vitro and in vivo neutralization profiles of monoclonal antibodies elicited by the receptor binding domain of the ancestral SARS-CoV-2. J Med Virol 2023;95:e28673. [PMID: 36916782 PMCID: PMC10189799 DOI: 10.1002/jmv.28673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 03/16/2023]
83
Newby ML, Fogarty CA, Allen JD, Butler J, Fadda E, Crispin M. Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics. J Mol Biol 2023;435:167928. [PMID: 36565991 PMCID: PMC9769069 DOI: 10.1016/j.jmb.2022.167928] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/25/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
84
Kuo HC, Kuo KC, Du PX, Keskin BB, Su WY, Ho TS, Tsai PS, Pau CH, Shih HC, Huang YH, Weng KP, Syu GD. Profiling humoral immunity after mixing and matching COVID-19 vaccines using SARS-CoV-2 variant protein microarrays. Mol Cell Proteomics 2023;22:100507. [PMID: 36787877 PMCID: PMC9922205 DOI: 10.1016/j.mcpro.2023.100507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/16/2023]  Open
85
Ching WY, Adhikari P, Jawad B, Podgornik R. Towards Quantum-Chemical Level Calculations of SARS-CoV-2 Spike Protein Variants of Concern by First Principles Density Functional Theory. Biomedicines 2023;11:517. [PMID: 36831053 PMCID: PMC9953097 DOI: 10.3390/biomedicines11020517] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]  Open
86
Characterization of a Vesicular Stomatitis Virus-Vectored Recombinant Virus Bearing Spike Protein of SARS-CoV-2 Delta Variant. Microorganisms 2023;11:microorganisms11020431. [PMID: 36838396 PMCID: PMC9960918 DOI: 10.3390/microorganisms11020431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/29/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023]  Open
87
Jiang H, Liu R, Wang L, Wang X, Zhang M, Lin S, Cao Z, Wu F, Liu Y, Liu J. Chiral-Selective Antigen-Presentation by Supramolecular Chiral Polymer Micelles. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023;35:e2208157. [PMID: 36398497 DOI: 10.1002/adma.202208157] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/14/2022] [Indexed: 06/16/2023]
88
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: 19] [Impact Index Per Article: 9.5] [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]
89
Saville JW, Mannar D, Zhu X, Berezuk AM, Cholak S, Tuttle KS, Vahdatihassani F, Subramaniam S. Structural analysis of receptor engagement and antigenic drift within the BA.2 spike protein. Cell Rep 2023;42:111964. [PMID: 36640338 PMCID: PMC9812370 DOI: 10.1016/j.celrep.2022.111964] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/10/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023]  Open
90
Almendro-Vázquez P, Laguna-Goya R, Paz-Artal E. Defending against SARS-CoV-2: The T cell perspective. Front Immunol 2023;14:1107803. [PMID: 36776863 PMCID: PMC9911802 DOI: 10.3389/fimmu.2023.1107803] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/16/2023] [Indexed: 01/28/2023]  Open
91
Arruda HR, Lima TM, Alvim RG, Victorio FB, Abreu DP, Marsili FF, Cruz KD, Marques MA, Sosa-Acosta P, Quinones-Vega M, de S. Guedes J, Nogueira FC, Silva JL, Castilho LR, de Oliveira GA. Conformational stability of SARS-CoV-2 glycoprotein spike variants. iScience 2023;26:105696. [PMID: 36465857 PMCID: PMC9710096 DOI: 10.1016/j.isci.2022.105696] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/18/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022]  Open
92
Ma R, Zhang Y, Zhang Y, Li X, Ji Z. The Relationship between the Transmission of Different SARS-CoV-2 Strains and Air Quality: A Case Study in China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023;20:ijerph20031943. [PMID: 36767307 PMCID: PMC9916065 DOI: 10.3390/ijerph20031943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/07/2023] [Accepted: 01/17/2023] [Indexed: 06/11/2023]
93
Bendall EE, Callear AP, Getz A, Goforth K, Edwards D, Monto AS, Martin ET, Lauring AS. Rapid transmission and tight bottlenecks constrain the evolution of highly transmissible SARS-CoV-2 variants. Nat Commun 2023;14:272. [PMID: 36650162 PMCID: PMC9844183 DOI: 10.1038/s41467-023-36001-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023]  Open
94
Haddad-Boubaker S, Arbi M, Souiai O, Chouikha A, Fares W, Edington K, Sims S, Camma C, Lorusso A, Diagne MM, Diallo A, Boubaker IBB, Ferjani S, Mastouri M, Mhalla S, Karray H, Gargouri S, Bahri O, Trabelsi A, Kallala O, Hannachi N, Chaabouni Y, Smaoui H, Meftah K, Bouhalila SB, Foughali S, Zribi M, Lamari A, Touzi H, Safer M, Alaya NB, Kahla AB, Gdoura M, Triki H. The Delta variant wave in Tunisia: Genetic diversity, spatio-temporal distribution and evidence of the spread of a divergent AY.122 sub-lineage. Front Public Health 2023;10:990832. [PMID: 36684874 PMCID: PMC9846204 DOI: 10.3389/fpubh.2022.990832] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 12/09/2022] [Indexed: 01/06/2023]  Open
95
Jin X, Sun X, Chai Y, Bai Y, Li Y, Hao T, Qi J, Song H, Wong CCL, Gao GF. Structural characterization of SARS-CoV-2 dimeric ORF9b reveals potential fold-switching trigger mechanism. SCIENCE CHINA. LIFE SCIENCES 2023;66:152-164. [PMID: 36184694 PMCID: PMC9527070 DOI: 10.1007/s11427-022-2168-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/20/2022] [Indexed: 11/06/2022]
96
Neamtu A, Mocci F, Laaksonen A, Barroso da Silva FL. Towards an optimal monoclonal antibody with higher binding affinity to the receptor-binding domain of SARS-CoV-2 spike proteins from different variants. Colloids Surf B Biointerfaces 2023;221:112986. [PMID: 36375294 PMCID: PMC9617679 DOI: 10.1016/j.colsurfb.2022.112986] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/13/2022] [Accepted: 10/27/2022] [Indexed: 11/13/2022]
97
Li Y, Xu S, Ye Q, Chi H, Guo Z, Chen J, Wu M, Fan B, Li B, Qin C, Liu Z. Rational Development of Hypervalent Glycan Shield-Binding Nanoparticles with Broad-Spectrum Inhibition against Fatal Viruses Including SARS-CoV-2 Variants. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023;10:e2202689. [PMID: 36377484 PMCID: PMC9839850 DOI: 10.1002/advs.202202689] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 09/22/2022] [Indexed: 05/31/2023]
98
Li M, Ren Y, Aw ZQ, Chen B, Yang Z, Lei Y, Cheng L, Liang Q, Hong J, Yang Y, Chen J, Wong YH, Wei J, Shan S, Zhang S, Ge J, Wang R, Dong JZ, Chen Y, Shi X, Zhang Q, Zhang Z, Chu JJH, Wang X, Zhang L. Broadly neutralizing and protective nanobodies against SARS-CoV-2 Omicron subvariants BA.1, BA.2, and BA.4/5 and diverse sarbecoviruses. Nat Commun 2022;13:7957. [PMID: 36575191 PMCID: PMC9792944 DOI: 10.1038/s41467-022-35642-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022]  Open
99
Zhu R, Canena D, Sikora M, Klausberger M, Seferovic H, Mehdipour AR, Hain L, Laurent E, Monteil V, Wirnsberger G, Wieneke R, Tampé R, Kienzl NF, Mach L, Mirazimi A, Oh YJ, Penninger JM, Hummer G, Hinterdorfer P. Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level. Nat Commun 2022;13:7926. [PMID: 36566234 PMCID: PMC9789309 DOI: 10.1038/s41467-022-35641-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/14/2022] [Indexed: 12/25/2022]  Open
100
Kwon HJ, Kosikova M, Tang W, Ortega-Rodriguez U, Radvak P, Xiang R, Mercer KE, Muskhelishvili L, Davis K, Ward JM, Kosik I, Holly J, Kang I, Yewdell JW, Plant EP, Chen WH, Shriver MC, Barnes RS, Pasetti MF, Zhou B, Wentworth DE, Xie H. Enhanced virulence and waning vaccine-elicited antibodies account for breakthrough infections caused by SARS-CoV-2 delta and beyond. iScience 2022;25:105507. [PMID: 36373096 PMCID: PMC9635945 DOI: 10.1016/j.isci.2022.105507] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/05/2022] [Accepted: 11/01/2022] [Indexed: 11/08/2022]  Open
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