Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement

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1. 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
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4. Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies
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7. Omicron BA.1 breakthrough infections in inactivated COVID-19 vaccine recipients induced distinct pattern of antibody and T cell responses to different Omicron sublineages
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8. An age-cohort simulation model for generating COVID-19 scenarios: A study from Ireland's pandemic response
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9. Variations in O-Glycosylation Patterns Influence Viral Pathogenicity, Infectivity, and Transmissibility in SARS-CoV-2 Variants
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10. Single-Molecule Investigation of the Binding Interface Stability of SARS-CoV-2 Variants with ACE2
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11. SARS-CoV-2 Omicron: Viral Evolution, Immune Evasion, and Alternative Durable Therapeutic Strategies
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12. IFN-λ uniquely promotes CD8 T cell immunity against SARS-CoV-2 relative to type I IFN
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13. Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein and potentially drive the genesis of Omicron variants
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15. The spike glycoprotein of highly pathogenic human coronaviruses: structural insights for understanding infection, evolution and inhibition
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16. Infection, pathology and interferon treatment of the SARS-CoV-2 Omicron BA.1 variant in juvenile, adult and aged Syrian hamsters
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17. Overcoming variant mutation-related impacts on viral sequencing and detection methodologies
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18. Distinct Conformations of SARS-CoV-2 Omicron Spike Protein and Its Interaction with ACE2 and Antibody
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19. Polyvalent Nano-Lectin Potently Neutralizes SARS-CoV-2 by Targeting Glycans on the Viral Spike Protein
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20. Impact of BA.1, BA.2, and BA.4/BA.5 Omicron Mutations on Therapeutic Monoclonal Antibodies
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21. How Do Point Mutations Enhancing the Basic Character of the RBDs of SARS-CoV-2 Variants Affect Their Transmissibility and Infectivity Capacities?
    A. Barre, B. Klonjkowski, H. Benoist, P. Rougé · 2022 · Viruses
22. Germinal center–mediated broadening of B cell responses to SARS-CoV-2 booster immunization
    Sameer Kumar Malladi, Deepika Jaiswal, Baoling Ying, Wafaa B. Alsoussi, Tamarand L. Darling, Bernadeta Dadonaite, Alesandro Civljak, Stephen C. Horvath, Julian Q. Zhou, Wooseob Kim et al. · 2025 · Science Immunology
23. Frustration-driven allosteric regulation and signal transmission in the SARS-CoV-2 spike omicron trimer structures: a crosstalk of the omicron mutation sites allosterically regulates tradeoffs of protein stability and conformational adaptability
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24. Evolutionary progression of collective mutations in Omicron sub-lineages towards efficient RBD-hACE2: Allosteric communications between and within viral and human proteins
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25. Omicron B.1.1.529 variant infections associated with severe disease are uncommon in a COVID-19 under-vaccinated, high SARS-CoV-2 seroprevalence population in Malawi
    Upendo L. Mseka, Jonathan J. Mandolo, Kenneth Nyoni, Oscar Divala, Dzinkambani Moffat Kambalame, Daniel Mapemba, Moses Kamzati, Innocent Chibwe, Marc Henrion, Kingsley Manda et al. · 2022 · EClinicalMedicine
26. Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern
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27. Artificial intelligence-based HDX (AI-HDX) prediction reveals fundamental characteristics to protein dynamics: Mechanisms on SARS-CoV-2 immune escape
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28. Tuning the immune response: sulfated archaeal glycolipid archaeosomes as an effective vaccine adjuvant for induction of humoral and cell-mediated immunity towards the SARS-CoV-2 Omicron variant of concern
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29. Effectiveness of homologous or heterologous immunization regimens against SARS-CoV-2 after two doses of inactivated COVID-19 vaccine: A systematic review and meta-analysis
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30. Modulation of SARS-CoV-2 spike binding to ACE2 through conformational selection
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31. IFN-γ-mediated control of SARS-CoV-2 infection through nitric oxide
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32. Impact of COVID-19 on the global hospitality industry: a brief review of current academic literature and meta-analysis to determine primary qualitative themes
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33. SARS‐CoV‐2 evolves to reduce but not abolish neutralizing action
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34. Maturation of SARS-CoV-2 Spike-specific memory B cells drives resilience to viral escape
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35. Cross-Linking Mass Spectrometry Uncovers Interactions Between High-Density Lipoproteins and the SARS-CoV-2 Spike Glycoprotein
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36. 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
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37. Molecular basis of SARS-CoV-2 Omicron variant receptor engagement and antibody evasion and neutralization
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38. Compensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA.1
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39. Enhanced virulence and waning vaccine-elicited antibodies account for breakthrough infections caused by SARS-CoV-2 delta and beyond
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40. SARS-CoV-2 spike host cell surface exposure promoted by a COPI sorting inhibitor
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41. Antibodies to S2 domain of SARS-CoV-2 spike protein in Moderna mRNA vaccinated subjects sustain antibody-dependent NK cell-mediated cell cytotoxicity against Omicron BA.1
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42. Infection kinetics, syncytia formation, and inflammatory biomarkers as predictive indicators for the pathogenicity of SARS-CoV-2 Variants of Concern in Calu-3 cells
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43. SARS‐CoV‐2 infection induces thymic atrophy mediated by IFN‐γ in hACE2 transgenic mice
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44. Exploring conformational landscapes and binding mechanisms of convergent evolution for the SARS-CoV-2 spike Omicron variant complexes with the ACE2 receptor using AlphaFold2-based structural ensembles and molecular dynamics simulations
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45. Quantitative Characterization and Prediction of the Binding Determinants and Immune Escape Hotspots for Groups of Broadly Neutralizing Antibodies Against Omicron Variants: Atomistic Modeling of the SARS-CoV-2 Spike Complexes with Antibodies
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47. A Systematic Review on the Emergence of Omicron Variant and Recent Advancement in Therapies
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48. Molecular dynamics study on the strengthening behavior of Delta and Omicron SARS-CoV-2 spike RBD improved receptor-binding affinity
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49. A broadly neutralizing monoclonal antibody overcomes the mutational landscape of emerging SARS-CoV-2 variants of concern
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51. Structure-based design of a SARS-CoV-2 Omicron-specific inhibitor
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57. Conformational dynamics of SARS-CoV-2 Omicron spike trimers during fusion activation at single molecule resolution
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63. The Omicron Variant of the Sars-Cov-2 Virus As the Dominant Agent of a New Risk of Disease amid the COVID-19 Pandemic
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79. Molecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response
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84. Across-the-board review on Omicron SARS-CoV-2 variant
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89. Structural basis of Omicron immune evasion: A comparative computational study
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93. Spike Protein Genetic Evolution in Patients at High Risk of Severe Coronavirus Disease 2019 Treated by Monoclonal Antibodies
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