Omicron (B.1.1.529) - A new heavily mutated variant: Mapped location and probable properties of its mutations with an emphasis on S-glycoprotein

Chakraborty, Chiranjib; Bhattacharya, Manojit; Sharma, Ashish Ranjan; Mallik, Bidyut

doi:10.1016/j.ijbiomac.2022.07.254

Cited by 43 publications

(23 citation statements)

References 99 publications

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“…Efforts are being made over time to develop the next-generation vaccine and mutation-proof vaccines [ 28 , 140 , 141 ]. At the same time, it has been observed that the Omicron variant and its sub-variant possess a very high number of mutations [ 27 , 29 , 120 ]. These mutations provide three significant properties to the Omicron variant.…”

Section: Discussionmentioning

confidence: 99%

“…Several mutations have been observed in the newly developed variants which alter the binding region of nAb, leading to antibody escape [ 117 , 118 ]. In the Omicron case, several mutations have been noted in the nAb binding region of the S protein, especially in RBD and NTD, which cause the nAb escape phenomenon [ 13 , 19 , 27 , 28 , 29 , 119 , 120 ]. Therefore, we can say that the Omicron variant possesses a partial vaccine escape ability.…”

Section: Immune Escape Of Emerging Omicron Variant and Its Sub-variantmentioning

confidence: 99%

“…Scientists are facing a real challenge to finding therapeutic antibodies against the Omicron variant because the therapeutic antibody escapes their neutralization efficacy due to certain properties of the Omicron variant [ 120 , 136 ]. Due to this, several scientists have tried to evaluate therapeutic antibodies against the Omicron variant over time and assess their efficacy of naturalization ( Table 3 ).…”

Section: Antiviral Drugs and Antibody-based Therapeutics Against The ...mentioning

confidence: 99%

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A Detailed Overview of SARS-CoV-2 Omicron: Its Sub-Variants, Mutations and Pathophysiology, Clinical Characteristics, Immunological Landscape, Immune Escape, and Therapies

Chatterjee

Bhattacharya

Nag

et al. 2023

Viruses

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136

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The COVID-19 pandemic has created significant concern for everyone. Recent data from many worldwide reports suggest that most infections are caused by the Omicron variant and its sub-lineages, dominating all the previously emerged variants. The numerous mutations in Omicron’s viral genome and its sub-lineages attribute it a larger amount of viral fitness, owing to the alteration of the transmission and pathophysiology of the virus. With a rapid change to the viral structure, Omicron and its sub-variants, namely BA.1, BA.2, BA.3, BA.4, and BA.5, dominate the community with an ability to escape the neutralization efficiency induced by prior vaccination or infections. Similarly, several recombinant sub-variants of Omicron, namely XBB, XBD, and XBF, etc., have emerged, which a better understanding. This review mainly entails the changes to Omicron and its sub-lineages due to it having a higher number of mutations. The binding affinity, cellular entry, disease severity, infection rates, and most importantly, the immune evading potential of them are discussed in this review. A comparative analysis of the Delta variant and the other dominating variants that evolved before Omicron gives the readers an in-depth understanding of the landscape of Omicron’s transmission and infection. Furthermore, this review discusses the range of neutralization abilities possessed by several approved antiviral therapeutic molecules and neutralizing antibodies which are functional against Omicron and its sub-variants. The rapid evolution of the sub-variants is causing infections, but the broader aspect of their transmission and neutralization has not been explored. Thus, the scientific community should adopt an elucidative approach to obtain a clear idea about the recently emerged sub-variants, including the recombinant variants, so that effective neutralization with vaccines and drugs can be achieved. This, in turn, will lead to a drop in the number of cases and, finally, an end to the pandemic.

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Section: Discussionmentioning

confidence: 99%

Section: Immune Escape Of Emerging Omicron Variant and Its Sub-variantmentioning

confidence: 99%

Section: Antiviral Drugs and Antibody-based Therapeutics Against The ...mentioning

confidence: 99%

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A Detailed Overview of SARS-CoV-2 Omicron: Its Sub-Variants, Mutations and Pathophysiology, Clinical Characteristics, Immunological Landscape, Immune Escape, and Therapies

Chatterjee

Bhattacharya

Nag

et al. 2023

Viruses

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136

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“…As of 8 September 2021, 1449 3D macro-molecular structural forms of SARS-CoV-2 have been solved and deposited in PDB. SARS-CoV-2 variants are developing due to diversified mutations [ 23 , 24 , 25 , 26 , 27 , 28 , 29 ]. During the SARS-CoV-2 mutation, the robustness and plasticity of the proteins change, which affects the overall functionality of the domains, especially the functional mechanisms of proteins [ 30 ].…”

Section: Introductionmentioning

confidence: 99%

Integrative Bioinformatics Approaches Indicate a Particular Pattern of Some SARS-CoV-2 and Non-SARS-CoV-2 Proteins

et al. 2022

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Pattern recognition plays a critical role in integrative bioinformatics to determine the structural patterns of proteins of viruses such as SARS-CoV-2. This study identifies the pattern of SARS-CoV-2 proteins to depict the structure–function relationships of the protein alphabets of SARS-CoV-2 and COVID-19. The assembly enumeration algorithm, Anisotropic Network Model, Gaussian Network Model, Markovian Stochastic Model, and image comparison protein-like alphabets were used. The distance score was the lowest with 22 for “I” and highest with 40 for “9”. For post-processing and decision, two protein alphabets “C” (PDB ID: 6XC3) and “S” (PDB ID: 7OYG) were evaluated to understand the structural, functional, and evolutionary relationships, and we found uniqueness in the functionality of proteins. Here, models were constructed using “SARS-CoV-2 proteins” (12 numbers) and “non-SARS-CoV-2 proteins” (14 numbers) to create two words, “SARS-CoV-2” and “COVID-19”. Similarly, we developed two slogans: “Vaccinate the world against COVID-19” and “Say no to SARS-CoV-2”, which were made with the proteins structure. It might generate vaccine-related interest to broad reader categories. Finally, the evolutionary process appears to enhance the protein structure smoothly to provide suitable functionality shaped by natural selection.

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“…Among them, seven mutations are from RBD and one from outside RBD. The seven RBD mutations are G496S, S477N, K417N, E484A, Q493K, Y505H, and N501Y, and the one outside RBD mutation is D614G [ 6 ]. Chen et al also found mutational escape of the Omicron variant.…”

mentioning

confidence: 99%

Immediate need for next-generation and mutation-proof vaccine to protect against current emerging Omicron sublineages and future SARS-CoV-2 variants: An urgent call for researchers and vaccine companies – Correspondence

Chakraborty

Bhattacharya²,

Sharma³

et al. 2022

International Journal of Surgery

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Omicron (B.1.1.529) - A new heavily mutated variant: Mapped location and probable properties of its mutations with an emphasis on S-glycoprotein

Cited by 43 publications

References 99 publications

A Detailed Overview of SARS-CoV-2 Omicron: Its Sub-Variants, Mutations and Pathophysiology, Clinical Characteristics, Immunological Landscape, Immune Escape, and Therapies

A Detailed Overview of SARS-CoV-2 Omicron: Its Sub-Variants, Mutations and Pathophysiology, Clinical Characteristics, Immunological Landscape, Immune Escape, and Therapies

Integrative Bioinformatics Approaches Indicate a Particular Pattern of Some SARS-CoV-2 and Non-SARS-CoV-2 Proteins

Immediate need for next-generation and mutation-proof vaccine to protect against current emerging Omicron sublineages and future SARS-CoV-2 variants: An urgent call for researchers and vaccine companies – Correspondence

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