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For: Starr TN, Greaney AJ, Addetia A, Hannon WW, Choudhary MC, Dingens AS, Li JZ, Bloom JD. Prospective mapping of viral mutations that escape antibodies used to treat COVID-19. Science 2021;371:850-854. [PMID: 33495308 PMCID: PMC7963219 DOI: 10.1126/science.abf9302] [Citation(s) in RCA: 595] [Impact Index Per Article: 148.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/19/2021] [Indexed: 12/13/2022]
Number Cited by Other Article(s)
51
Hussein HAM, Thabet AA, Wardany AA, El-Adly AM, Ali M, Hassan MEA, Abdeldayem MAB, Mohamed ARMA, Sobhy A, El-Mokhtar MA, Afifi MM, Fathy SM, Sultan S. SARS-CoV-2 outbreak: role of viral proteins and genomic diversity in virus infection and COVID-19 progression. Virol J 2024;21:75. [PMID: 38539202 PMCID: PMC10967059 DOI: 10.1186/s12985-024-02342-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 03/12/2024] [Indexed: 05/15/2024]  Open
52
Karim F, Riou C, Bernstein M, Jule Z, Lustig G, van Graan S, Keeton RS, Upton JL, Ganga Y, Khan K, Reedoy K, Mazibuko M, Govender K, Thambu K, Ngcobo N, Venter E, Makhado Z, Hanekom W, von Gottberg A, Hoque M, Karim QA, Abdool Karim SS, Manickchund N, Magula N, Gosnell BI, Lessells RJ, Moore PL, Burgers WA, de Oliveira T, Moosa MYS, Sigal A. Clearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation. Nat Commun 2024;15:2360. [PMID: 38491050 PMCID: PMC10943233 DOI: 10.1038/s41467-024-46673-2] [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: 08/10/2023] [Accepted: 02/27/2024] [Indexed: 03/18/2024]  Open
53
Majoumo-Mbe F, Sangbong NA, Tadjong Tcho A, Namba-Nzanguim CT, Simoben CV, Eni DB, Alhaji Isa M, Poli ANR, Cassel J, Salvino JM, Montaner LJ, Tietjen I, Ntie-Kang F. 5-chloro-3-(2-(2,4-dinitrophenyl) hydrazono)indolin-2-one: synthesis, characterization, biochemical and computational screening against SARS-CoV-2. CHEMICKE ZVESTI 2024;78:3431-3441. [PMID: 38685970 PMCID: PMC11055700 DOI: 10.1007/s11696-023-03274-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 12/04/2023] [Indexed: 05/02/2024]
54
Powers JM, Leist SR, Mallory ML, Yount BL, Gully KL, Zweigart MR, Bailey AB, Sheahan TP, Harkema JR, Baric RS. Divergent pathogenetic outcomes in BALB/c mice following Omicron subvariant infection. Virus Res 2024;341:199319. [PMID: 38224840 PMCID: PMC10835285 DOI: 10.1016/j.virusres.2024.199319] [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: 09/30/2023] [Revised: 01/02/2024] [Accepted: 01/12/2024] [Indexed: 01/17/2024]
55
Gerashchenko GV, Hryshchenko NV, Melnichuk NS, Marchyshak TV, Chernushyn SY, Demchyshina IV, Chernenko LM, Kuzin IV, Tkachuk ZY, Kashuba VI, Tukalo MA. Genetic characteristics of SARS-CoV-2 virus variants observed upon three waves of the COVID-19 pandemic in Ukraine between February 2021-January 2022. Heliyon 2024;10:e25618. [PMID: 38380034 PMCID: PMC10877268 DOI: 10.1016/j.heliyon.2024.e25618] [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: 04/25/2023] [Revised: 12/06/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024]  Open
56
Korosec CS, Wahl LM, Heffernan JM. Within-host evolution of SARS-CoV-2: how often are de novo mutations transmitted from symptomatic infections? Virus Evol 2024;10:veae006. [PMID: 38425472 PMCID: PMC10904108 DOI: 10.1093/ve/veae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/20/2023] [Accepted: 01/12/2024] [Indexed: 03/02/2024]  Open
57
Carr CR, Crawford KHD, Murphy M, Galloway JG, Haddox HK, Matsen FA, Andersen KG, King NP, Bloom JD. Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.579020. [PMID: 38370709 PMCID: PMC10871245 DOI: 10.1101/2024.02.05.579020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
58
Gupta S, Gupta D, Bhatnagar S. Analysis of SARS-CoV-2 genome evolutionary patterns. Microbiol Spectr 2024;12:e0265423. [PMID: 38197644 PMCID: PMC10846092 DOI: 10.1128/spectrum.02654-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/20/2023] [Indexed: 01/11/2024]  Open
59
Zaccaria M, Genovese L, Lawhorn BE, Dawson W, Joyal AS, Hu J, Autissier P, Nakajima T, Johnson WE, Fofana I, Farzan M, Momeni B. Predicting potential SARS-CoV-2 mutations of concern via full quantum mechanical modelling. J R Soc Interface 2024;21:20230614. [PMID: 38320601 PMCID: PMC10846948 DOI: 10.1098/rsif.2023.0614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/05/2024] [Indexed: 02/08/2024]  Open
60
Acar DD, Witkowski W, Wejda M, Wei R, Desmet T, Schepens B, De Cae S, Sedeyn K, Eeckhaut H, Fijalkowska D, Roose K, Vanmarcke S, Poupon A, Jochmans D, Zhang X, Abdelnabi R, Foo CS, Weynand B, Reiter D, Callewaert N, Remaut H, Neyts J, Saelens X, Gerlo S, Vandekerckhove L. Integrating artificial intelligence-based epitope prediction in a SARS-CoV-2 antibody discovery pipeline: caution is warranted. EBioMedicine 2024;100:104960. [PMID: 38232633 PMCID: PMC10803917 DOI: 10.1016/j.ebiom.2023.104960] [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: 05/01/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024]  Open
61
Ketaren NE, Mast FD, Fridy PC, Olivier JP, Sanyal T, Sali A, Chait BT, Rout MP, Aitchison JD. Nanobody repertoire generated against the spike protein of ancestral SARS-CoV-2 remains efficacious against the rapidly evolving virus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.14.549041. [PMID: 37503298 PMCID: PMC10369967 DOI: 10.1101/2023.07.14.549041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
62
Cianfarini C, Hassler L, Wysocki J, Hassan A, Nicolaescu V, Elli D, Gula H, Ibrahim AM, Randall G, Henkin J, Batlle D. Soluble Angiotensin-Converting Enzyme 2 Protein Improves Survival and Lowers Viral Titers in Lethal Mouse Model of Severe Acute Respiratory Syndrome Coronavirus Type 2 Infection with the Delta Variant. Cells 2024;13:203. [PMID: 38334597 PMCID: PMC10854654 DOI: 10.3390/cells13030203] [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: 12/22/2023] [Revised: 01/19/2024] [Accepted: 01/20/2024] [Indexed: 02/10/2024]  Open
63
Li K, Verma A, Li P, Ortiz ME, Hawkins GM, Schnicker NJ, Szachowicz PJ, Pezzulo AA, Wohlford-Lenane CL, Kicmal T, Meyerholz DK, Gallagher T, Perlman S, McCray PB. Adaptation of SARS-CoV-2 to ACE2H353K mice reveals new spike residues that drive mouse infection. J Virol 2024;98:e0151023. [PMID: 38168680 PMCID: PMC10804960 DOI: 10.1128/jvi.01510-23] [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: 09/27/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024]  Open
64
Wang D, Huot M, Mohanty V, Shakhnovich EI. Biophysical principles predict fitness of SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.23.549087. [PMID: 37577536 PMCID: PMC10418099 DOI: 10.1101/2023.07.23.549087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
65
Harari S, Miller D, Fleishon S, Burstein D, Stern A. Using big sequencing data to identify chronic SARS-Coronavirus-2 infections. Nat Commun 2024;15:648. [PMID: 38245511 PMCID: PMC10799923 DOI: 10.1038/s41467-024-44803-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024]  Open
66
Irvine EB, Reddy ST. Advancing Antibody Engineering through Synthetic Evolution and Machine Learning. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024;212:235-243. [PMID: 38166249 DOI: 10.4049/jimmunol.2300492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/20/2023] [Indexed: 01/04/2024]
67
Feng Y, Yi J, Yang L, Wang Y, Wen J, Zhao W, Kim P, Zhou X. COV2Var, a function annotation database of SARS-CoV-2 genetic variation. Nucleic Acids Res 2024;52:D701-D713. [PMID: 37897356 PMCID: PMC10767816 DOI: 10.1093/nar/gkad958] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/29/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023]  Open
68
Alfaleh MA, Alsulaiman RM, Almahboub SA, Nezamuldeen L, Zawawi A, Aljehani ND, Yasir M, Abdulal RH, Alkhaldi R, Helal A, Alamri SS, Malki J, Alhabbab RY, Abujamel TS, Alhakamy NA, Alnami A, Algaissi A, Hassanain M, Hashem AM. ACE2-Fc and DPP4-Fc decoy receptors against SARS-CoV-2 and MERS-CoV variants: a quick therapeutic option for current and future coronaviruses outbreaks. Antib Ther 2024;7:53-66. [PMID: 38371953 PMCID: PMC10873275 DOI: 10.1093/abt/tbad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 02/20/2024]  Open
69
Quezada A, Annapareddy A, Javanmardi K, Cooper J, Finkelstein IJ. Mammalian Antigen Display for Pandemic Countermeasures. Methods Mol Biol 2024;2762:191-216. [PMID: 38315367 DOI: 10.1007/978-1-0716-3666-4_12] [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] [Indexed: 02/07/2024]
70
Zhang L, Cao H, Medlin K, Pearson J, Aristotelous AC, Chen A, Wessler T, Forest MG. Computational Modeling Insights into Extreme Heterogeneity in COVID-19 Nasal Swab Data. Viruses 2023;16:69. [PMID: 38257769 PMCID: PMC10820884 DOI: 10.3390/v16010069] [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: 10/05/2023] [Revised: 12/20/2023] [Accepted: 12/23/2023] [Indexed: 01/24/2024]  Open
71
Gregory DA, Rushford C, Hunter T, Lin CH, Darby C, Niehues N, Semkiw E, Reynolds M, Wenzel J, Johnson MC. Continued selection on cryptic SARS-CoV-2 observed in Missouri wastewater. PLoS Pathog 2023;19:e1011688. [PMID: 38153929 PMCID: PMC10781090 DOI: 10.1371/journal.ppat.1011688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/10/2024] [Accepted: 12/18/2023] [Indexed: 12/30/2023]  Open
72
Lopez-Morales J, Vanella R, Appelt EA, Whillock S, Paulk AM, Shusta EV, Hackel BJ, Liu CC, Nash MA. Protein Engineering and High-Throughput Screening by Yeast Surface Display: Survey of Current Methods. SMALL SCIENCE 2023;3:2300095. [PMID: 39071103 PMCID: PMC11271970 DOI: 10.1002/smsc.202300095] [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: 06/19/2023] [Revised: 08/25/2023] [Indexed: 07/30/2024]  Open
73
Taylor AL, Starr TN. Deep mutational scans of XBB.1.5 and BQ.1.1 reveal ongoing epistatic drift during SARS-CoV-2 evolution. PLoS Pathog 2023;19:e1011901. [PMID: 38157379 PMCID: PMC10783747 DOI: 10.1371/journal.ppat.1011901] [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] [Received: 09/19/2023] [Revised: 01/11/2024] [Accepted: 12/14/2023] [Indexed: 01/03/2024]  Open
74
Gayvert K, McKay S, Lim WK, Baum A, Kyratsous C, Copin R, Atwal GS. Evolutionary trajectory of SARS-CoV-2 genome shifts during widespread vaccination and emergence of Omicron variant. NPJ VIRUSES 2023;1:5. [PMID: 40295667 PMCID: PMC11721106 DOI: 10.1038/s44298-023-00007-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/25/2023] [Indexed: 04/30/2025]
75
Schröder S, Richter A, Veith T, Emanuel J, Gudermann L, Friedmann K, Jeworowski LM, Mühlemann B, Jones TC, Müller MA, Corman VM, Drosten C. Characterization of intrinsic and effective fitness changes caused by temporarily fixed mutations in the SARS-CoV-2 spike E484 epitope and identification of an epistatic precondition for the evolution of E484A in variant Omicron. Virol J 2023;20:257. [PMID: 37940989 PMCID: PMC10633978 DOI: 10.1186/s12985-023-02154-4] [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: 06/23/2023] [Accepted: 08/08/2023] [Indexed: 11/10/2023]  Open
76
Yu S, Zheng X, Zhou Y, Gao Y, Zhou B, Zhao Y, Li T, Li Y, Mou J, Cui X, Yang Y, Li D, Chen M, Lavillette D, Meng G. Antibody-mediated spike activation promotes cell-cell transmission of SARS-CoV-2. PLoS Pathog 2023;19:e1011789. [PMID: 37948454 PMCID: PMC10664894 DOI: 10.1371/journal.ppat.1011789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 11/22/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023]  Open
77
Bhattacharya M, Chatterjee S, Lee SS, Dhama K, Chakraborty C. Antibody evasion associated with the RBD significant mutations in several emerging SARS-CoV-2 variants and its subvariants. Drug Resist Updat 2023;71:101008. [PMID: 37757651 DOI: 10.1016/j.drup.2023.101008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023]
78
Hannon WW, Bloom JD. dms-viz: Structure-informed visualizations for deep mutational scanning and other mutation-based datasets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.29.564578. [PMID: 37961289 PMCID: PMC10634933 DOI: 10.1101/2023.10.29.564578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
79
Erasmus MF, Ferrara F, D'Angelo S, Spector L, Leal-Lopes C, Teixeira AA, Sørensen J, Nagpal S, Perea-Schmittle K, Choudhary A, Honnen W, Calianese D, Antonio Rodriguez Carnero L, Cocklin S, Greiff V, Pinter A, Bradbury ARM. Insights into next generation sequencing guided antibody selection strategies. Sci Rep 2023;13:18370. [PMID: 37884618 PMCID: PMC10603065 DOI: 10.1038/s41598-023-45538-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023]  Open
80
Fang S, Lei C, Li M, Ming Y, Liu L, Zhou X, Li M. Collaborative effects of 2019-nCoV-Spike mutants on viral infectivity. Comput Struct Biotechnol J 2023;21:5125-5135. [PMID: 37920812 PMCID: PMC10618117 DOI: 10.1016/j.csbj.2023.10.030] [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: 07/06/2023] [Revised: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023]  Open
81
Ghoula M, Deyawe Kongmeneck A, Eid R, Camproux AC, Moroy G. Comparative Study of the Mutations Observed in the SARS-CoV-2 RBD Variants of Concern and Their Impact on the Interaction with the ACE2 Protein. J Phys Chem B 2023;127:8586-8602. [PMID: 37775095 PMCID: PMC10578311 DOI: 10.1021/acs.jpcb.3c01467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/20/2023] [Indexed: 10/01/2023]
82
Thadani NN, Gurev S, Notin P, Youssef N, Rollins NJ, Ritter D, Sander C, Gal Y, Marks DS. Learning from prepandemic data to forecast viral escape. Nature 2023;622:818-825. [PMID: 37821700 PMCID: PMC10599991 DOI: 10.1038/s41586-023-06617-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/06/2023] [Indexed: 10/13/2023]
83
Onigbinde S, Reyes CDG, Fowowe M, Daramola O, Atashi M, Bennett AI, Mechref Y. Variations in O-Glycosylation Patterns Influence Viral Pathogenicity, Infectivity, and Transmissibility in SARS-CoV-2 Variants. Biomolecules 2023;13:1467. [PMID: 37892149 PMCID: PMC10604390 DOI: 10.3390/biom13101467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/29/2023]  Open
84
Yoon J, Patrick JE, Ogbunugafor CB, Shoulders MD. Viral Evolution Shaped by Host Proteostasis Networks. Annu Rev Virol 2023;10:77-98. [PMID: 37071930 PMCID: PMC10543606 DOI: 10.1146/annurev-virology-100220-112120] [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] [Indexed: 04/20/2023]
85
Raiser F, Davis M, Adelglass J, Cai MR, Chau G, Cloney-Clark S, Eickhoff M, Kalkeri R, McKnight I, Plested J, Zhu M, Dunkle LM. Immunogenicity and safety of NVX-CoV2373 as a booster: A phase 3 randomized clinical trial in adults. Vaccine 2023;41:5965-5973. [PMID: 37652823 DOI: 10.1016/j.vaccine.2023.07.056] [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: 03/16/2023] [Revised: 07/25/2023] [Accepted: 07/25/2023] [Indexed: 09/02/2023]
86
Ho C, Nazarie WFWM, Lee PC. An In Silico Design of Peptides Targeting the S1/S2 Cleavage Site of the SARS-CoV-2 Spike Protein. Viruses 2023;15:1930. [PMID: 37766336 PMCID: PMC10536081 DOI: 10.3390/v15091930] [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: 08/16/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023]  Open
87
Shen H, Yang H. Binding of synthetic nanobodies to the SARS-CoV-2 receptor-binding domain: the importance of salt bridges. Phys Chem Chem Phys 2023;25:24129-24142. [PMID: 37655617 DOI: 10.1039/d3cp02628k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
88
Taylor AL, Starr TN. Deep mutational scans of XBB.1.5 and BQ.1.1 reveal ongoing epistatic drift during SARS-CoV-2 evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.11.557279. [PMID: 37745441 PMCID: PMC10515859 DOI: 10.1101/2023.09.11.557279] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
89
Curtis NC, Shin S, Hederman AP, Connor RI, Wieland-Alter WF, Ionov S, Boylston J, Rose J, Sakharkar M, Dorman DB, Dessaint JA, Gwilt LL, Crowley AR, Feldman J, Hauser BM, Schmidt AG, Ashare A, Walker LM, Wright PF, Ackerman ME, Lee J. Characterization of SARS-CoV-2 Convalescent Patients' Serological Repertoire Reveals High Prevalence of Iso-RBD Antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.08.556349. [PMID: 37745524 PMCID: PMC10515772 DOI: 10.1101/2023.09.08.556349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
90
Guo M, Xiong M, Peng J, Guan T, Su H, Huang Y, Yang CG, Li Y, Boraschi D, Pillaiyar T, Wang G, Yi C, Xu Y, Chen C. Multi-omics for COVID-19: driving development of therapeutics and vaccines. Natl Sci Rev 2023;10:nwad161. [PMID: 37936830 PMCID: PMC10627145 DOI: 10.1093/nsr/nwad161] [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: 11/27/2022] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 11/09/2023]  Open
91
Vanderlinden E, Boonen A, Noppen S, Schoofs G, Imbrechts M, Geukens N, Snoeck R, Stevaert A, Naesens L, Andrei G, Schols D. PRO-2000 exhibits SARS-CoV-2 antiviral activity by interfering with spike-heparin binding. Antiviral Res 2023;217:105700. [PMID: 37562608 DOI: 10.1016/j.antiviral.2023.105700] [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: 06/02/2023] [Revised: 07/29/2023] [Accepted: 08/06/2023] [Indexed: 08/12/2023]
92
Jin H, Cheng L, Gong Y, Zhu Y, Chong H, Zhang Z, He Y. Design of a bifunctional pan-sarbecovirus entry inhibitor targeting the cell receptor and viral fusion protein. J Virol 2023;97:e0019223. [PMID: 37578234 PMCID: PMC10506475 DOI: 10.1128/jvi.00192-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/02/2023] [Indexed: 08/15/2023]  Open
93
Lobinska G, Pilpel Y, Nowak MA. Evolutionary safety of lethal mutagenesis driven by antiviral treatment. PLoS Biol 2023;21:e3002214. [PMID: 37552682 PMCID: PMC10409280 DOI: 10.1371/journal.pbio.3002214] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 06/23/2023] [Indexed: 08/10/2023]  Open
94
Ladner JT, Sahl JW. Towards a post-pandemic future for global pathogen genome sequencing. PLoS Biol 2023;21:e3002225. [PMID: 37527248 PMCID: PMC10393143 DOI: 10.1371/journal.pbio.3002225] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]  Open
95
Kugathasan R, Sukhova K, Moshe M, Kellam P, Barclay W. Deep mutagenesis scanning using whole trimeric SARS-CoV-2 spike highlights the importance of NTD-RBD interactions in determining spike phenotype. PLoS Pathog 2023;19:e1011545. [PMID: 37535672 PMCID: PMC10426949 DOI: 10.1371/journal.ppat.1011545] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 08/15/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023]  Open
96
Flynn JM, Huang QYJ, Zvornicanin SN, Schneider-Nachum G, Shaqra AM, Yilmaz NK, Moquin SA, Dovala D, Schiffer CA, Bolon DN. Systematic Analyses of the Resistance Potential of Drugs Targeting SARS-CoV-2 Main Protease. ACS Infect Dis 2023;9:1372-1386. [PMID: 37390404 PMCID: PMC11161032 DOI: 10.1021/acsinfecdis.3c00125] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
97
Hamdy ME, El Deeb AH, Hagag NM, Shahein MA, Alaidi O, Hussein HA. Interspecies transmission of SARS CoV-2 with special emphasis on viral mutations and ACE-2 receptor homology roles. Int J Vet Sci Med 2023;11:55-86. [PMID: 37441062 PMCID: PMC10334861 DOI: 10.1080/23144599.2023.2222981] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 05/11/2023] [Accepted: 05/19/2023] [Indexed: 07/15/2023]  Open
98
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
99
Gomez-Gonzalez E, Muñoz O, Gomez-Martin JC, Aceituno-Castro J, Fernandez-Muñoz B, Navas-Garcia JM, Barriga-Rivera A, Fernandez-Lizaranzu I, Munoz-Gonzalez FJ, Parrilla-Giraldez R, Requena-Lancharro D, Gil-Gamboa P, Ramos JL, Rosell-Valle C, Gomez-Gonzalez C, Martin-Lopez M, Relimpio-Lopez MI, Perales-Esteve MA, Puppo-Moreno A, Garcia-Cozar FJ, Olvera-Collantes L, de Los Santos-Trigo S, Gomez E, Sanchez-Pernaute R, Padillo-Ruiz J, Marquez-Rivas J. Polarimetric imaging for the detection of synthetic models of SARS-CoV-2: A proof of concept. JOURNAL OF QUANTITATIVE SPECTROSCOPY & RADIATIVE TRANSFER 2023;302:108567. [PMID: 36945203 PMCID: PMC9987604 DOI: 10.1016/j.jqsrt.2023.108567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 03/04/2023] [Accepted: 03/04/2023] [Indexed: 06/18/2023]
100
Keng CT, Yogarajah T, Lee RCH, Muhammad IBH, Chia BS, Vasandani SR, Lim DS, Guo K, Wong YH, Mok CK, Chu JJH, Chew WL. AAV-CRISPR-Cas13 eliminates human enterovirus and prevents death of infected mice. EBioMedicine 2023;93:104682. [PMID: 37390772 PMCID: PMC10363442 DOI: 10.1016/j.ebiom.2023.104682] [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: 02/15/2023] [Revised: 06/13/2023] [Accepted: 06/13/2023] [Indexed: 07/02/2023]  Open
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