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, Chiranjib; Bhattacharya, Manojit; Sharma, Ashish Ranjan; Mohapatra, Ranjan K.; Chakraborty, Sandip; Pal, Soumen; Dhama, Kuldeep

doi:10.1016/j.ijsu.2022.106903

Cited by 12 publications

(14 citation statements)

References 10 publications

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“…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%

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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155

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

confidence: 99%

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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155

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“…Common side effects of the COVID-19 vaccines and statistics of Adverse Events Following Immunization (AEFIs) in Macau were presented in Tables 4 , 5 . The vaccines have succeeded in preventing severe disease or death, but more novel next-gen COVID-19 vaccines are still necessary for keeping people from catching and spreading the virus because SARS-CoV-2 has become more contagious and it is evolving to dodge the vaccines ( 7 , 22 , 23 ).…”

Section: Resultsmentioning

confidence: 99%

“…Compared with previous variants (including the Alpha, Beta, Gamma, and Delta variants of SARS-CoV-2, and the BA.1, BA.2., BA.3, BA.4 lineages of Omicron, etc.) ( 4 – 7 ), the latest BA.5 variant is better at evading the immune system and has become the most easily transmissible variant to date ( 5 , 8 ). It has gradually become the dominant strain of the SARS-CoV-2 virus in many parts of the world and has been associated with the rapidly escalating COVID-19 cases and hospitalizations.…”

Section: Introductionmentioning

confidence: 99%

Omicron subvariant BA.5 is highly contagious but containable: Successful experience from Macau

Wang

et al. 2023

Front. Public Health

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IntroductionDue to its high transmissibility and immune escape, Omicron subvariant BA.5 has become the dominant strain of the SARS-CoV-2 virus and led to escalating COVID-19 cases, how to cope with it becomes an urgent issue. A BA.5 infection surge burst out on 18 June 2022 and brought an unprecedented challenge to Macau, the most densely populated region worldwide. This study aimed to analyze the characteristics of this outbreak and summarize the useful anti-epidemic measures and experiences during this outbreak.MethodsAll data were obtained from the Government Portal of Macao SAR (https://www.gov.mo), and the Special Webpage Against Epidemics, the Macao Health Bureau (www.ssm.gov.mo). An epidemiologic study was performed to analyze epidemic outcomes, including the infection rate, the proportion of symptomatic cases, the case fatality ratio (CFR), etc. Data were analyzed using SPSS Version 20. A p-value <0.05 was considered statistically significant. The anti-epidemic measures and experience were reviewed and summarized.ResultsThe BA.5 outbreak resulted in 1,821 new cases, which was significantly more than the cumulative cases of the previous variants of COVID-19 in Macau. The symptomatic cases accounted for 38.71% of the total cases, which was higher than that of the previous variants. After 6-week concerted efforts, Macau effectively controlled the outbreak, with an infection rate of 0.27%, which was much lower than many BA.5-attacked regions. The CFR was approximately 0.86%, which was not statistically different from that of previous variants. Six victims were chronically ill senior elders and their vaccination rate was much lower than the average level. Macau took a comprehensive anti-epidemic strategy to win a quick victory against BA.5, especially the “relatively static” strategy that was first formulated and applied by Macau for the management of the COVID-19 pandemic. Successful experience showed that although BA.5 was highly contagious, it could be contained by comprehensive anti-epidemic measures, including adequate anti-epidemic preparation, herd immunity through vaccination, repeated mass nucleic acid tests and rapid antigen tests, KN-95 mask mandate, the “relatively static” strategy, precise prevention and control, epidemiological investigation and tracing, and traditional Chinese medicine treatment, etc.DiscussionIn Macau, compared with the previous subvariants, BA.5 is associated with increased transmissibility and a higher proportion of symptomatic cases, however, the risk of death remains similar, and the infection rate is much lower than that in many other BA.5-attacked regions. BA.5 is highly contagious but still containable, Macau's experience may offer hints for the regions experiencing the BA.5 waves to choose or adjust a more rational anti-epidemic strategy.

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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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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

Cited by 12 publications

References 10 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

Omicron subvariant BA.5 is highly contagious but containable: Successful experience from Macau

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

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