Deep Structural Analysis of Myriads of Omicron Sub-Variants Revealed Hotspot for Vaccine Escape Immunity

Gerardi, Valeria and Rohaim, Mohammed A. and Naggar, Rania F. El and Atasoy, Mustafa O. and Munir, Muhammad (2023) Deep Structural Analysis of Myriads of Omicron Sub-Variants Revealed Hotspot for Vaccine Escape Immunity. Vaccines, 11 (3): 668. ISSN 2076-393X

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Abstract

The emergence of the Omicron variant has reinforced the importance of continued SARS-CoV-2 evolution and its possible impact on vaccine effectiveness. Specifically, mutations in the receptor-binding domain (RBD) are critical to comprehend the flexibility and dynamicity of the viral interaction with the human agniotensin-converting enzyme 2 (hACE2) receptor. To this end, we have applied a string of deep structural and genetic analysis tools to map the substitution patterns in the S protein of major Omicron sub-variants (n = 51) with a primary focus on the RBD mutations. This head-to-head comparison of Omicron sub-variants revealed multiple simultaneous mutations that are attributed to antibody escape, and increased affinity and binding to hACE2. Our deep mapping of the substitution matrix indicated a high level of diversity at the N-terminal and RBD domains compared with other regions of the S protein, highlighting the importance of these two domains in a matched vaccination approach. Structural mapping identified highly variable mutations in the up confirmation of the S protein and at sites that critically define the function of the S protein in the virus pathobiology. These substitutional trends offer support in tracking mutations along the evolutionary trajectories of SAR-CoV-2. Collectively, the findings highlight critical areas of mutations across the major Omicron sub-variants and propose several hotspots in the S proteins of SARS-CoV-2 sub-variants to train the future design and development of COVID-19 vaccines.

Item Type:
Journal Article
Journal or Publication Title:
Vaccines
Uncontrolled Keywords:
/dk/atira/pure/subjectarea/asjc/2700/2725
Subjects:
?? pharmacology (medical)infectious diseasesdrug discoverypharmacologyimmunologyinfectious diseasespharmacology (medical)pharmacologydrug discoveryimmunology ??
ID Code:
189842
Deposited By:
Deposited On:
27 Mar 2023 13:30
Refereed?:
Yes
Published?:
Published
Last Modified:
22 Jul 2024 00:23