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Structural diversity of the SARS-CoV-2 Omicron spike.
<div class='caption-title'>Conformational diversity of the SARS-CoV-2 Omicron (B.1.1.529) S protein</div>
<div class='caption-title'>Intra-protomer communication through the NTD-to-RBD (N2R) linker</div>
Gobeil SM, Henderson R, Stalls V, Janowska K, Huang X, May A, Speakman M, Beaudoin E, Manne K, Li D, Parks R, Barr M, Deyton M, Martin M, Mansouri K, Edwards RJ, Eaton A, Montefiori DC, Sempowski GD, Saunders KO, Wiehe K, Williams W, Korber B, Haynes BF, Acharya P
OpenAccess logo Mol Cell 82 2050-2068.e6 (2022)

Cited: 106 times
EuropePMC logo PMID: 35447081

Abstract

Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. Spike conformation plays an essential role in SARS-CoV-2 evolution via changes in receptor-binding domain (RBD) and neutralizing antibody epitope presentation, affecting virus transmissibility and immune evasion. Here, we determine cryo-EM structures of the Omicron and Delta spikes to understand the conformational impacts of mutations in each. The Omicron spike structure revealed an unusually tightly packed RBD organization with long range impacts that were not observed in the Delta spike. Binding and crystallography revealed increased flexibility at the functionally critical fusion peptide site in the Omicron spike. These results reveal a highly evolved Omicron spike architecture with possible impacts on its high levels of immune evasion and transmissibility.

Articles - 7tp8 mentioned but not cited (2)

  1. Structural diversity of the SARS-CoV-2 Omicron spike. Gobeil SM, Henderson R, Stalls V, Janowska K, Huang X, May A, Speakman M, Beaudoin E, Manne K, Li D, Parks R, Barr M, Deyton M, Martin M, Mansouri K, Edwards RJ, Eaton A, Montefiori DC, Sempowski GD, Saunders KO, Wiehe K, Williams W, Korber B, Haynes BF, Acharya P. Mol Cell 82 2050-2068.e6 (2022)
  2. Progressive membrane-binding mechanism of SARS-CoV-2 variant spike proteins. Overduin M, Kervin TA, Tran A. iScience 25 104722 (2022)


Reviews citing this publication (13)

  1. Omicron variant (B.1.1.529) and its sublineages: What do we know so far amid the emergence of recombinant variants of SARS-CoV-2? Dhawan M, Saied AA, Mitra S, Alhumaydhi FA, Emran TB, Wilairatana P. Biomed Pharmacother 154 113522 (2022)
  2. PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology. Westbrook JD, Young JY, Shao C, Feng Z, Guranovic V, Lawson CL, Vallat B, Adams PD, Berrisford JM, Bricogne G, Diederichs K, Joosten RP, Keller P, Moriarty NW, Sobolev OV, Velankar S, Vonrhein C, Waterman DG, Kurisu G, Berman HM, Burley SK, Peisach E. J Mol Biol 434 167599 (2022)
  3. Structural Plasticity and Immune Evasion of SARS-CoV-2 Spike Variants. Ghimire D, Han Y, Lu M. Viruses 14 1255 (2022)
  4. Could a Lower Toll-like Receptor (TLR) and NF-κB Activation Due to a Changed Charge Distribution in the Spike Protein Be the Reason for the Lower Pathogenicity of Omicron? Kircheis R, Planz O. Int J Mol Sci 23 5966 (2022)
  5. Evolution of the SARS-CoV-2 Omicron spike. Parsons RJ, Acharya P. Cell Rep 42 113444 (2023)
  6. Insight into SARS-CoV-2 Omicron variant immune escape possibility and variant independent potential therapeutic opportunities. Alam MS. Heliyon 9 e13285 (2023)
  7. Mechanism and evolution of human ACE2 binding by SARS-CoV-2 spike. Wrobel AG. Curr Opin Struct Biol 81 102619 (2023)
  8. Distinct Conformations of SARS-CoV-2 Omicron Spike Protein and Its Interaction with ACE2 and Antibody. Lee M, Major M, Hong H. Int J Mol Sci 24 3774 (2023)
  9. Smart healthcare: A prospective future medical approach for COVID-19. Yang DM, Chang TJ, Hung KF, Wang ML, Cheng YF, Chiang SH, Chen MF, Liao YT, Lai WQ, Liang KH. J Chin Med Assoc 86 138-146 (2023)
  10. Variants of SARS-CoV-2: Influences on the Vaccines' Effectiveness and Possible Strategies to Overcome Their Consequences. Rabaan AA, Al-Ahmed SH, Albayat H, Alwarthan S, Alhajri M, Najim MA, AlShehail BM, Al-Adsani W, Alghadeer A, Abduljabbar WA, Alotaibi N, Alsalman J, Gorab AH, Almaghrabi RS, Zaidan AA, Aldossary S, Alissa M, Alburaiky LM, Alsalim FM, Thakur N, Verma G, Dhawan M. Medicina (Kaunas) 59 507 (2023)
  11. Structural understanding of SARS-CoV-2 virus entry to host cells. Le K, Kannappan S, Kim T, Lee JH, Lee HR, Kim KK. Front Mol Biosci 10 1288686 (2023)
  12. Cryo-electron microscopy in the study of virus entry and infection. Dutta M, Acharya P. Front Mol Biosci 11 1429180 (2024)
  13. The D Gene in CDR H3 Determines a Public Class of Human Antibodies to SARS-CoV-2. Yuan M, Wilson IA. Vaccines (Basel) 12 467 (2024)

Articles citing this publication (91)

  1. ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies. Low JS, Jerak J, Tortorici MA, McCallum M, Pinto D, Cassotta A, Foglierini M, Mele F, Abdelnabi R, Weynand B, Noack J, Montiel-Ruiz M, Bianchi S, Benigni F, Sprugasci N, Joshi A, Bowen JE, Stewart C, Rexhepaj M, Walls AC, Jarrossay D, Morone D, Paparoditis P, Garzoni C, Ferrari P, Ceschi A, Neyts J, Purcell LA, Snell G, Corti D, Lanzavecchia A, Veesler D, Sallusto F. Science 377 735-742 (2022)
  2. Structural and functional impact by SARS-CoV-2 Omicron spike mutations. Zhang J, Cai Y, Lavine CL, Peng H, Zhu H, Anand K, Tong P, Gautam A, Mayer ML, Rits-Volloch S, Wang S, Sliz P, Wesemann DR, Yang W, Seaman MS, Lu J, Xiao T, Chen B. Cell Rep 39 110729 (2022)
  3. Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function. Martin DP, Lytras S, Lucaci AG, Maier W, Grüning B, Shank SD, Weaver S, MacLean OA, Orton RJ, Lemey P, Boni MF, Tegally H, Harkins GW, Scheepers C, Bhiman JN, Everatt J, Amoako DG, San JE, Giandhari J, Sigal A, NGS-SA, Williamson C, Hsiao NY, von Gottberg A, De Klerk A, Shafer RW, Robertson DL, Wilkinson RJ, Sewell BT, Lessells R, Nekrutenko A, Greaney AJ, Starr TN, Bloom JD, Murrell B, Wilkinson E, Gupta RK, de Oliveira T, Kosakovsky Pond SL. Mol Biol Evol 39 msac061 (2022)
  4. Cryo-EM structures of SARS-CoV-2 Omicron BA.2 spike. Stalls V, Lindenberger J, Gobeil SM, Henderson R, Parks R, Barr M, Deyton M, Martin M, Janowska K, Huang X, May A, Speakman M, Beaudoin E, Kraft B, Lu X, Edwards RJ, Eaton A, Montefiori DC, Williams WB, Saunders KO, Wiehe K, Haynes BF, Acharya P. Cell Rep 39 111009 (2022)
  5. Compensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA.1. Moulana A, Dupic T, Phillips AM, Chang J, Nieves S, Roffler AA, Greaney AJ, Starr TN, Bloom JD, Desai MM. Nat Commun 13 7011 (2022)
  6. Atlas of currently available human neutralizing antibodies against SARS-CoV-2 and escape by Omicron sub-variants BA.1/BA.1.1/BA.2/BA.3. Huang M, Wu L, Zheng A, Xie Y, He Q, Rong X, Han P, Du P, Han P, Zhang Z, Zhao R, Jia Y, Li L, Bai B, Hu Z, Hu S, Niu S, Hu Y, Liu H, Liu B, Cui K, Li W, Zhao X, Liu K, Qi J, Wang Q, Gao GF. Immunity 55 1501-1514.e3 (2022)
  7. Identification of a conserved S2 epitope present on spike proteins from all highly pathogenic coronaviruses. Silva RP, Huang Y, Nguyen AW, Hsieh CL, Olaluwoye OS, Kaoud TS, Wilen RE, Qerqez AN, Park JG, Khalil AM, Azouz LR, Le KC, Bohanon AL, DiVenere AM, Liu Y, Lee AG, Amengor DA, Shoemaker SR, Costello SM, Padlan EA, Marqusee S, Martinez-Sobrido L, Dalby KN, D'Arcy S, McLellan JS, Maynard JA. Elife 12 e83710 (2023)
  8. Determinants of Spike infectivity, processing, and neutralization in SARS-CoV-2 Omicron subvariants BA.1 and BA.2. Pastorio C, Zech F, Noettger S, Jung C, Jacob T, Sanderson T, Sparrer KMJ, Kirchhoff F. Cell Host Microbe 30 1255-1268.e5 (2022)
  9. An updated atlas of antibody evasion by SARS-CoV-2 Omicron sub-variants including BQ.1.1 and XBB. He Q, Wu L, Xu Z, Wang X, Xie Y, Chai Y, Zheng A, Zhou J, Qiao S, Huang M, Shang G, Zhao X, Feng Y, Qi J, Gao GF, Wang Q. Cell Rep Med 4 100991 (2023)
  10. Essential role of TMPRSS2 in SARS-CoV-2 infection in murine airways. Iwata-Yoshikawa N, Kakizaki M, Shiwa-Sudo N, Okura T, Tahara M, Fukushi S, Maeda K, Kawase M, Asanuma H, Tomita Y, Takayama I, Matsuyama S, Shirato K, Suzuki T, Nagata N, Takeda M. Nat Commun 13 6100 (2022)
  11. SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization. Mannar D, Saville JW, Sun Z, Zhu X, Marti MM, Srivastava SS, Berezuk AM, Zhou S, Tuttle KS, Sobolewski MD, Kim A, Treat BR, Da Silva Castanha PM, Jacobs JL, Barratt-Boyes SM, Mellors JW, Dimitrov DS, Li W, Subramaniam S. Nat Commun 13 4696 (2022)
  12. SARS-CoV-2 spike N-terminal domain modulates TMPRSS2-dependent viral entry and fusogenicity. Meng B, Datir R, Choi J, CITIID-NIHR Bioresource COVID-19 Collaboration, Bradley JR, Smith KGC, Lee JH, Gupta RK. Cell Rep 40 111220 (2022)
  13. The SARS-CoV-2 spike S375F mutation characterizes the Omicron BA.1 variant. Kimura I, Yamasoba D, Nasser H, Zahradnik J, Kosugi Y, Wu J, Nagata K, Uriu K, Tanaka YL, Ito J, Shimizu R, Tan TS, Butlertanaka EP, Asakura H, Sadamasu K, Yoshimura K, Ueno T, Takaori-Kondo A, Schreiber G, Genotype to Phenotype Japan (G2P-Japan) Consortium, Toyoda M, Shirakawa K, Irie T, Saito A, Nakagawa S, Ikeda T, Sato K. iScience 25 105720 (2022)
  14. SARS-CoV-2 Omicron Variant Binds to Human Cells More Strongly than the Wild Type: Evidence from Molecular Dynamics Simulation. Nguyen HL, Thai NQ, Nguyen PH, Li MS. J Phys Chem B 126 4669-4678 (2022)
  15. Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein. 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. Nat Commun 14 1421 (2023)
  16. Association Between Vaccination Coverage Disparity and the Dynamics of the COVID-19 Delta and Omicron Waves in the US. Cuadros DF, Moreno CM, Musuka G, Miller FD, Coule P, MacKinnon NJ. Front Med (Lausanne) 9 898101 (2022)
  17. Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics. Newby ML, Fogarty CA, Allen JD, Butler J, Fadda E, Crispin M. J Mol Biol 435 167928 (2023)
  18. Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level. 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. Nat Commun 13 7926 (2022)
  19. A Bispecific Antibody Targeting RBD and S2 Potently Neutralizes SARS-CoV-2 Omicron and Other Variants of Concern. Yuan M, Chen X, Zhu Y, Dong X, Liu Y, Qian Z, Ye L, Liu P. J Virol 96 e0077522 (2022)
  20. Broadly Neutralizing Antibodies to SARS-CoV-2 Provide Novel Insights Into the Neutralization of Variants and Other Human Coronaviruses. Bajpai P, Singh V, Chandele A, Kumar S. Front Cell Infect Microbiol 12 928279 (2022)
  21. The Spike Protein of SARS-CoV-2 Is Adapting Because of Selective Pressures. López-Cortés GI, Palacios-Pérez M, Veledíaz HF, Hernández-Aguilar M, López-Hernández GR, Zamudio GS, José MV. Vaccines (Basel) 10 864 (2022)
  22. Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. Verkhivker G, Agajanian S, Kassab R, Krishnan K. Int J Mol Sci 23 4376 (2022)
  23. Probing Mechanisms of Binding and Allostery in the SARS-CoV-2 Spike Omicron Variant Complexes with the Host Receptor: Revealing Functional Roles of the Binding Hotspots in Mediating Epistatic Effects and Communication with Allosteric Pockets. Verkhivker G, Agajanian S, Kassab R, Krishnan K. Int J Mol Sci 23 11542 (2022)
  24. The potential of Beta variant containing COVID booster vaccines for chasing Omicron in 2022. Sridhar S, Chicz RM, Warren W, Tartaglia J, Savarino S, Gurunathan S, Toussaint JF. Nat Commun 13 5794 (2022)
  25. Bibliometric Analysis of Publications on the Omicron Variant from 2020 to 2022 in the Scopus Database Using R and VOSviewer. Ejaz H, Zeeshan HM, Ahmad F, Bukhari SNA, Anwar N, Alanazi A, Sadiq A, Junaid K, Atif M, Abosalif KOA, Iqbal A, Hamza MA, Younas S. Int J Environ Res Public Health 19 12407 (2022)
  26. Protein Scaffold-Based Multimerization of Soluble ACE2 Efficiently Blocks SARS-CoV-2 Infection In Vitro and In Vivo. Kayabolen A, Akcan U, Özturan D, Ulbegi-Polat H, Sahin GN, Pinarbasi-Degirmenci N, Bayraktar C, Soyler G, Sarayloo E, Nurtop E, Ozer B, Guney-Esken G, Barlas T, Yildirim IS, Dogan O, Karahuseyinoglu S, Lack NA, Kaya M, Albayrak C, Can F, Solaroglu I, Bagci-Onder T. Adv Sci (Weinh) 9 e2201294 (2022)
  27. 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. Verkhivker G, Alshahrani M, Gupta G. Viruses 15 1143 (2023)
  28. Dual-Affinity Graphene Sheets for High-Resolution Cryo-Electron Microscopy. Cheng H, Zheng L, Liu N, Huang C, Xu J, Lu Y, Cui X, Xu K, Hou Y, Tang J, Zhang Z, Li J, Ni X, Chen Y, Peng H, Wang HW. J Am Chem Soc 145 8073-8081 (2023)
  29. A broadly neutralizing monoclonal antibody overcomes the mutational landscape of emerging SARS-CoV-2 variants of concern. Parray HA, Narayanan N, Garg S, Rizvi ZA, Shrivastava T, Kushwaha S, Singh J, Murugavelu P, Anantharaj A, Mehdi F, Raj N, Singh S, Dandotiya J, Lukose A, Jamwal D, Kumar S, Chiranjivi AK, Dhyani S, Mishra N, Kumar S, Jakhar K, Sonar S, Panchal AK, Tripathy MR, Chowdhury SR, Ahmed S, Samal S, Mani S, Bhattacharyya S, Das S, Sinha S, Luthra K, Batra G, Sehgal D, Medigeshi GR, Sharma C, Awasthi A, Garg PK, Nair DT, Kumar R. PLoS Pathog 18 e1010994 (2022)
  30. Cryomicroscopy in situ: what is the smallest molecule that can be directly identified without labels in a cell? Russo CJ, Dickerson JL, Naydenova K. Faraday Discuss 240 277-302 (2022)
  31. Population immunity predicts evolutionary trajectories of SARS-CoV-2. Meijers M, Ruchnewitz D, Eberhardt J, Łuksza M, Lässig M. Cell 186 5151-5164.e13 (2023)
  32. Mutations in S2 subunit of SARS-CoV-2 Omicron spike strongly influence its conformation, fusogenicity, and neutralization sensitivity. Kumar S, Delipan R, Chakraborty D, Kanjo K, Singh R, Singh N, Siddiqui S, Tyagi A, Jha V, Thakur KG, Pandey R, Varadarajan R, Ringe RP. J Virol 97 e0092223 (2023)
  33. Site of vulnerability on SARS-CoV-2 spike induces broadly protective antibody against antigenically distinct Omicron subvariants. Changrob S, Halfmann PJ, Liu H, Torres JL, McGrath JJC, Ozorowski G, Li L, Wilbanks GD, Kuroda M, Maemura T, Huang M, Zheng NY, Turner HL, Erickson SA, Fu Y, Yasuhara A, Singh G, Monahan B, Mauldin J, Srivastava K, Simon V, Krammer F, Sather DN, Ward AB, Wilson IA, Kawaoka Y, Wilson PC. J Clin Invest 133 e166844 (2023)
  34. [Strengthening the prevention and treatment of Omicron infection in children]. Jiao FY, Ma L. Zhongguo Dang Dai Er Ke Za Zhi 24 345-349 (2022)
  35. Adaptive variations in SARS-CoV-2 spike proteins: effects on distinct virus-cell entry stages. Qing E, Gallagher T. mBio 14 e0017123 (2023)
  36. Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes. Zhang X, Li Z, Zhang Y, Liu Y, Wang J, Liu B, Chen Q, Wang Q, Fu L, Wang P, Zhong X, Jin L, Yan Q, Chen L, He J, Zhao J, Xiong X. Life Sci Alliance 6 e202201796 (2023)
  37. Network analysis uncovers the communication structure of SARS-CoV-2 spike protein identifying sites for immunogen design. Manrique PD, Chakraborty S, Henderson R, Edwards RJ, Mansbach R, Nguyen K, Stalls V, Saunders C, Mansouri K, Acharya P, Korber B, Gnanakaran S. iScience 26 105855 (2023)
  38. Omicron mutations increase interdomain interactions and reduce epitope exposure in the SARS-CoV-2 spike. Wieczór M, Tang PK, Orozco M, Cossio P. iScience 26 105981 (2023)
  39. Temperature Influences the Interaction between SARS-CoV-2 Spike from Omicron Subvariants and Human ACE2. Gong SY, Ding S, Benlarbi M, Chen Y, Vézina D, Marchitto L, Beaudoin-Bussières G, Goyette G, Bourassa C, Bo Y, Medjahed H, Levade I, Pazgier M, Côté M, Richard J, Prévost J, Finzi A. Viruses 14 2178 (2022)
  40. Computational analysis of the sequence-structure relation in SARS-CoV-2 spike protein using protein contact networks. Guzzi PH, di Paola L, Puccio B, Lomoio U, Giuliani A, Veltri P. Sci Rep 13 2837 (2023)
  41. Effects of N-glycan modifications on spike expression, virus infectivity, and neutralization sensitivity in ancestral compared to Omicron SARS-CoV-2 variants. Lusvarghi S, Stauft CB, Vassell R, Williams B, Baha H, Wang W, Neerukonda SN, Wang T, Weiss CD. PLoS Pathog 19 e1011788 (2023)
  42. Long-term variations and potency of neutralizing antibodies against Omicron subvariants after CoronaVac-inactivated booster: A 7-month follow-up study. Li X, Yin Y, Cui Q, Huang W, Zou Q, Shen T. J Med Virol 95 e28279 (2023)
  43. Novel chimeric proteins mimicking SARS-CoV-2 spike epitopes with broad inhibitory activity. Cano-Muñoz M, Polo-Megías D, Cámara-Artigas A, Gavira JA, López-Rodríguez MJ, Laumond G, Schmidt S, Demiselle J, Bahram S, Moog C, Conejero-Lara F. Int J Biol Macromol 222 2467-2478 (2022)
  44. Analyzing the immunogenicity of bivalent booster vaccinations in healthcare workers: The SWITCH ON trial protocol. Tan NH, Sablerolles RSG, Rietdijk WJR, Goorhuis A, Postma DF, Visser LG, Bogers S, Geers D, Zaeck LM, Koopmans MPG, Dalm VASH, Kootstra NA, Huckriede ALW, van Baarle D, Lafeber M, GeurtsvanKessel CH, de Vries RD, van der Kuy PM. Front Immunol 13 1067749 (2022)
  45. Caveats of chimpanzee ChAdOx1 adenovirus-vectored vaccines to boost anti-SARS-CoV-2 protective immunity in mice. Cervantes-Torres J, Cabello-Gutiérrez C, Ayón-Núñez DA, Soldevila G, Olguin-Alor R, Diaz G, Acero G, Segura-Velázquez R, Huerta L, Gracia-Mora I, Cobos L, Pérez-Tapia M, Almagro JC, Suárez-Güemes F, Bobes RJ, Fragoso G, Sciutto E, Laclette JP. Appl Microbiol Biotechnol 108 179 (2024)
  46. Coarse-Grained Molecular Simulations and Ensemble-Based Mutational Profiling of Protein Stability in the Different Functional Forms of the SARS-CoV-2 Spike Trimers: Balancing Stability and Adaptability in BA.1, BA.2 and BA.2.75 Variants. Verkhivker G, Alshahrani M, Gupta G. Int J Mol Sci 24 6642 (2023)
  47. Comparative Analysis of Conformational Dynamics and Systematic Characterization of Cryptic Pockets in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB.1 Spike Complexes with the ACE2 Host Receptor: Confluence of Binding and Structural Plasticity in Mediating Networks of Conserved Allosteric Sites. Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Viruses 15 2073 (2023)
  48. Engineered immunogens to elicit antibodies against conserved coronavirus epitopes. Kapingidza AB, Marston DJ, Harris C, Wrapp D, Winters K, Mielke D, Xiaozhi L, Yin Q, Foulger A, Parks R, Barr M, Newman A, Schäfer A, Eaton A, Flores JM, Harner A, Catanzaro NJ, Mallory ML, Mattocks MD, Beverly C, Rhodes B, Mansouri K, Van Itallie E, Vure P, Dunn B, Keyes T, Stanfield-Oakley S, Woods CW, Petzold EA, Walter EB, Wiehe K, Edwards RJ, Montefiori DC, Ferrari G, Baric R, Cain DW, Saunders KO, Haynes BF, Azoitei ML. Nat Commun 14 7897 (2023)
  49. Exploring Conformational Landscapes and Cryptic Binding Pockets in Distinct Functional States of the SARS-CoV-2 Omicron BA.1 and BA.2 Trimers: Mutation-Induced Modulation of Protein Dynamics and Network-Guided Prediction of Variant-Specific Allosteric Binding Sites. Verkhivker G, Alshahrani M, Gupta G. Viruses 15 2009 (2023)
  50. Heterologous boost with mRNA vaccines against SARS-CoV-2 Delta/Omicron variants following an inactivated whole-virus vaccine. Lu C, Zhang Y, Liu X, Hou F, Cai R, Yu Z, Liu F, Yang G, Ding J, Xu J, Hua X, Cheng X, Pan X, Liu L, Lin K, Wang Z, Li X, Lu J, Zhang Q, Li Y, Hu C, Fan H, Liu X, Wang H, Jia R, Xu F, Wang X, Huang H, Zhao R, Li J, Cheng H, Jia W, Yang X. Antiviral Res 212 105556 (2023)
  51. 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. Xiao S, Alshahrani M, Gupta G, Tao P, Verkhivker G. J Chem Inf Model 63 5272-5296 (2023)
  52. Non-covalent cyclic peptides simultaneously targeting Mpro and NRP1 are highly effective against Omicron BA.2.75. Yin S, Mei S, Li Z, Xu Z, Wu Y, Chen X, Liu D, Niu MM, Li J. Front Pharmacol 13 1037993 (2022)
  53. Omicron Spike Protein is Vulnerable to Reduction. Yao Z, Geng B, Marcon E, Pu S, Tang H, Merluza J, Bello A, Snider J, Lu P, Wood H, Stagljar I. J Mol Biol 435 168128 (2023)
  54. Recurrent SARS-CoV-2 mutations at Spike D796 evade antibodies from pre-Omicron convalescent and vaccinated subjects. Elko EA, Mead HL, Nelson GA, Zaia JA, Ladner JT, Altin JA. Microbiol Spectr 12 e0329123 (2024)
  55. SARS-CoV-2 spike variants differ in their allosteric responses to linoleic acid. Oliveira ASF, Shoemark DK, Davidson AD, Berger I, Schaffitzel C, Mulholland AJ. J Mol Cell Biol 15 mjad021 (2023)
  56. Ancestral Lineage of SARS-CoV-2 Is More Stable in Human Biological Fluids than Alpha, Beta, and Omicron Variants of Concern. Kwon T, Gaudreault NN, Meekins DA, McDowell CD, Cool K, Richt JA. Microbiol Spectr 11 e0330122 (2023)
  57. Research Support, Non-U.S. Gov't 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). de Souza AS, de Souza RF, Guzzo CR. J Comput Aided Mol Des 37 585-606 (2023)
  58. Evolutionary trajectory of receptor binding specificity and promiscuity of the spike protein of SARS-CoV-2. Planchais C, Reyes-Ruiz A, Lacombe R, Zarantonello A, Lecerf M, Revel M, Roumenina LT, Atanasov BP, Mouquet H, Dimitrov JD. Protein Sci 31 e4447 (2022)
  59. In Silico Analyses Indicate a Lower Potency for Dimerization of TLR4/MD-2 as the Reason for the Lower Pathogenicity of Omicron Compared to Wild-Type Virus and Earlier SARS-CoV-2 Variants. Kircheis R. Int J Mol Sci 25 5451 (2024)
  60. Long-term passaging of pseudo-typed SARS-CoV-2 reveals the breadth of monoclonal and bispecific antibody cocktails. Ma H, Zong HF, Liu JJ, Yue YL, Ke Y, Liao YJ, Tang HN, Wang L, Wang SS, Yuan YS, Wu MY, Bian YL, Zhang BH, Yin HY, Jiang H, Sun T, Han L, Xie YQ, Zhu JW. Acta Pharmacol Sin 44 1455-1463 (2023)
  61. Multimodal, broadly neutralizing antibodies against SARS-CoV-2 identified by high-throughput native pairing of BCRs from bulk B cells. Keitany GJ, Rubin BER, Garrett ME, Musa A, Tracy J, Liang Y, Ebert P, Moore AJ, Guan J, Eggers E, Lescano N, Brown R, Carbo A, Al-Asadi H, Ching T, Day A, Harris R, Linkem C, Popov D, Wilkins C, Li L, Wang J, Liu C, Chen L, Dines JN, Atyeo C, Alter G, Baldo L, Sherwood A, Howie B, Klinger M, Yusko E, Robins HS, Benzeno S, Gilbert AE. Cell Chem Biol 30 1377-1389.e8 (2023)
  62. Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes. Zehr JD, Kosakovsky Pond SL, Millet JK, Olarte-Castillo XA, Lucaci AG, Shank SD, Ceres KM, Choi A, Whittaker GR, Goodman LB, Stanhope MJ. Virus Evol 9 vead019 (2023)
  63. Preserved recognition of Omicron spike following COVID-19 messenger RNA vaccination in pregnancy. Bartsch YC, Atyeo C, Kang J, Cai Y, Chen B, Gray KJ, Edlow AG, Alter G. Am J Obstet Gynecol 227 493.e1-493.e7 (2022)
  64. 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. Verkhivker G, Alshahrani M, Gupta G, Xiao S, Tao P. Phys Chem Chem Phys 25 21245-21266 (2023)
  65. Structural Basis for the Enhanced Infectivity and Immune Evasion of Omicron Subvariants. Li Y, Shen Y, Zhang Y, Yan R. Viruses 15 1398 (2023)
  66. Structural and biochemical rationale for Beta variant protein booster vaccine broad cross-neutralization of SARS-CoV-2. Bruch EM, Zhu S, Szymkowicz L, Blake T, Kiss T, James DA, Rak A, Narayan K, Balmer MT, Chicz RM. Sci Rep 14 2038 (2024)
  67. The Effect of Select SARS-CoV-2 N-Linked Glycan and Variant of Concern Spike Protein Mutations on C-Type Lectin-Receptor-Mediated Infection. Bains A, Guan W, LiWang PJ. Viruses 15 1901 (2023)
  68. Transient transfection and purification of SARS-CoV-2 spike protein from mammalian cells. Stalls V, Janowska K, Acharya P. STAR Protoc 3 101603 (2022)
  69. Conformational Behavior of SARS-Cov-2 Spike Protein Variants: Evolutionary Jumps in Sequence Reverberate in Structural Dynamic Differences. Triveri A, Casali E, Frasnetti E, Doria F, Frigerio F, Cinquini F, Pavoni S, Moroni E, Marchetti F, Serapian SA, Colombo G. J Chem Theory Comput 19 2120-2134 (2023)
  70. De Novo Human Angiotensin-Converting Enzyme 2 Decoy NL-CVX1 Protects Mice From Severe Disease After Severe Acute Respiratory Syndrome Coronavirus 2 Infection. Rebelo M, Tang C, Coelho AR, Labão-Almeida C, Schneider MM, Tatalick L, Ruivo P, de Miranda MP, Gomes A, Carvalho T, Walker MJ, Ausserwoeger H, Pedro Simas J, Veldhoen M, Knowles TPJ, Silva DA, Shoultz D, Bernardes GJL. J Infect Dis 228 723-733 (2023)
  71. Ensemble-Based Mutational Profiling and Network Analysis of the SARS-CoV-2 Spike Omicron XBB Lineages for Interactions with the ACE2 Receptor and Antibodies: Cooperation of Binding Hotspots in Mediating Epistatic Couplings Underlies Binding Mechanism and Immune Escape. Raisinghani N, Alshahrani M, Gupta G, Verkhivker G. Int J Mol Sci 25 4281 (2024)
  72. Impact of mutations defining SARS-CoV-2 Omicron subvariants BA.2.12.1 and BA.4/5 on Spike function and neutralization. Pastorio C, Noettger S, Nchioua R, Zech F, Sparrer KMJ, Kirchhoff F. iScience 26 108299 (2023)
  73. Integrating Conformational Dynamics and Perturbation-Based Network Modeling for Mutational Profiling of Binding and Allostery in the SARS-CoV-2 Spike Variant Complexes with Antibodies: Balancing Local and Global Determinants of Mutational Escape Mechanisms. Verkhivker G, Agajanian S, Kassab R, Krishnan K. Biomolecules 12 964 (2022)
  74. Oxalic acid blocked the binding of spike protein from SARS-CoV-2 Delta (B.1.617.2) and Omicron (B.1.1.529) variants to human angiotensin-converting enzymes 2. Wang M, Yan H, Chen L, Wang Y, Li L, Zhang H, Miao L. PLoS One 18 e0285722 (2023)
  75. Persistent topological Laplacian analysis of SARS-CoV-2 variants. Wei X, Chen J, Wei GW. J Comput Biophys Chem 22 569-587 (2023)
  76. Role of N343 glycosylation on the SARS-CoV-2 S RBD structure and co-receptor binding across variants of concern. Ives CM, Nguyen L, Fogarty CA, Harbison AM, Durocher Y, Klassen J, Fadda E. Elife 13 RP95708 (2024)
  77. SARS-CoV-2 Omicron Subvariants Balance Host Cell Membrane, Receptor, and Antibody Docking via an Overlapping Target Site. Overduin M, Bhat RK, Kervin TA. Viruses 15 447 (2023)
  78. SARS-CoV-2 Omicron XBB lineage spike structures, conformations, antigenicity, and receptor recognition. Zhang QE, Lindenberger J, Parsons RJ, Thakur B, Parks R, Park CS, Huang X, Sammour S, Janowska K, Spence TN, Edwards RJ, Martin M, Williams WB, Gobeil S, Montefiori DC, Korber B, Saunders KO, Haynes BF, Henderson R, Acharya P. Mol Cell 84 2747-2764.e7 (2024)
  79. Temporary COVID-19 Specialized Hospital: Management Strategies for Public Health Emergencies. Tian B, Ning Z, Tu P. J Multidiscip Healthc 16 1699-1704 (2023)
  80. A chimeric adenovirus-vectored vaccine based on Beta spike and Delta RBD confers a broad-spectrum neutralization against Omicron-included SARS-CoV-2 variants. Hong W, Lei H, Peng D, Huang Y, He C, Yang J, Zhou Y, Liu J, Pan X, Que H, Alu A, Chen L, Ai J, Qin F, Wang B, Ao D, Zeng Z, Hao Y, Zhang Y, Huang X, Ye C, Fu M, He X, Bi Z, Han X, Luo M, Hu H, Cheng W, Dong H, Lei J, Chen L, Zhou X, Wang W, Lu G, Shen G, Yang L, Yang J, Li J, Wang Z, Song X, Sun Q, Lu S, Wang Y, Cheng P, Wei X. MedComm (2020) 5 e539 (2024)
  81. APOBEC3-related mutations in the spike protein-encoding region facilitate SARS-CoV-2 evolution. Shen J, Xu X, Fan J, Chen H, Zhao Y, Huang W, Liu W, Zhang Z, Cui Q, Li Q, Niu Z, Jiang D, Cao G. Heliyon 10 e32139 (2024)
  82. Assessing pH-Dependent Conformational Changes in the Fusion Peptide Proximal Region of the SARS-CoV-2 Spike Glycoprotein. Stepanenko D, Wang Y, Simmerling C. Viruses 16 1066 (2024)
  83. Association of Social Vulnerability and COVID-19 Mortality Rates in Texas between 15 March 2020, and 21 July 2022: An Ecological Analysis. Nyachoti DO, Ranjit N, Ramphul R, Whigham LD, Springer AE. Int J Environ Res Public Health 20 6985 (2023)
  84. Excess mortality in Ukraine during the course of COVID-19 pandemic in 2020-2021. Shishkin A, Lhewa P, Yang C, Gankin Y, Chowell G, Norris M, Skums P, Kirpich A. Sci Rep 13 6917 (2023)
  85. Fusing Peptide Epitopes for Advanced Multiplex Serological Testing for SARS-CoV-2 Antibody Detection. Aldoukhi AH, Bilalis P, Alhattab DM, Valle-Pérez AU, Susapto HH, Pérez-Pedroza R, Backhoff-García E, Alsawaf SM, Alshehri S, Boshah H, Alrashoudi AA, Aljabr WA, Alaamery M, Alrashed M, Hasanato RM, Farzan RA, Alsubki RA, Moretti M, Abedalthagafi MS, Hauser CAE. ACS Bio Med Chem Au 4 37-52 (2024)
  86. Genomic surveillance of genes encoding the SARS-CoV-2 spike protein to monitor for emerging variants on Jeju Island, Republic of Korea. Ha YR, Kim HJ, Park JS, Chung YS. Front Microbiol 14 1170766 (2023)
  87. Infection with the SARS-CoV-2 Omicron variant in children with congenital heart disease: A case series study during Shanghai epidemic. Yang Y, Wu Y, Zhang W, Cao Q, Zhang H, Zhang H, Dong W. Front Cardiovasc Med 9 1001780 (2022)
  88. Micro-second time-resolved X-ray single-molecule internal motions of SARS-CoV-2 spike variants. Sasaki D, Arai T, Yang Y, Kuramochi M, Furuyama W, Nanbo A, Sekiguchi H, Morone N, Mio K, Sasaki YC. Biochem Biophys Rep 38 101712 (2024)
  89. Oral administration of a recombinant modified RBD antigen of SARS-CoV-2 as a possible immunostimulant for the care of COVID-19. Valdez-Cruz NA, Rosiles-Becerril D, Martínez-Olivares CE, García-Hernández E, Cobos-Marín L, Garzón D, López-Salas FE, Zavala G, Luviano A, Olvera A, Alagón A, Ramírez OT, Trujillo-Roldán MA. Microb Cell Fact 23 41 (2024)
  90. The S2 subunit of spike encodes diverse targets for functional antibody responses to SARS-CoV-2. Guenthoer J, Garrett ME, Lilly M, Depierreux DM, Ruiz F, Chi M, Stoddard CI, Chohan V, Yaffe ZA, Sung K, Ralph D, Chu HY, Matsen FA, Overbaugh J. PLoS Pathog 20 e1012383 (2024)
  91. The evolution of vaccine hesitancy through the COVID-19 pandemic: A semi-structured interview study on booster and bivalent doses. Parsons Leigh J, FitzGerald EA, Moss SJ, Cherak MS, Brundin-Mather R, Dodds A, Stelfox HT, Dubé È, Fiest KM, Halperin DM, Ahmed SB, MacDonald SE, Straus SE, Manca T, Ng Kamstra J, Soo A, Longmore S, Kupsch S, Sept B, Halperin SA. Hum Vaccin Immunother 20 2316417 (2024)


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