Epitopes Determination for OMICRON: The COVID-19 New Variant

Rehman, Saba; Hayat, Faisal Salih; Norin, Sadia; Wang, Li; Rahman, Siddiq Ur; Haq, Noor ul

doi:10.17582/journal.pjz/20220712070711

Cited by 1 publication

(1 citation statement)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The amino acid analyses for the S2 subunit revealed that mutations N764K and N856K provide cleavage sites for SKI-1/S1P and prevent the internal fusion peptide from being exposed to the membrane fusion and syncytia formation. The protein convertase SKI-1/S1P is expressed in the bronchus and nasopharynx but not in the lungs, which may explain differing tissue tropisms [ 90 , 91 , 92 , 93 , 94 ]. Sub-variants BA.1 and BA.1.1 showed N764K and N856K mutations, whereas BA.2, group 3, and group 7 showed only N764K.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2023

View full text Add to dashboard Cite

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.

show abstract