Extensive genetic diversity with novel mutations in spike glycoprotein of severe acute respiratory syndrome coronavirus 2, Bangladesh in late 2020

Afrin, Sultana Zahura; Paul, Shyamal Kumar; Begum, Jahan Ara; Nasreen, S A; Ahmed, Salma; Ahmad, Fahad; Aziz, Muhammad; Parvin, Rokshana; Aung, Meiji Soe; Kobayashi, Nobumichi

doi:10.1016/j.nmni.2021.100889

Cited by 10 publications

(7 citation statements)

References 27 publications

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“…The mutation was observed in the Delta For the first time, it was noted in variants isolated from India (156,157). This mutation was also reported in Bangladesh (179). The mutation augments infectivity and may help in the immune escape phenomena of the virus.…”

Section: P681rmentioning

confidence: 84%

A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations

et al. 2022

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The infective SARS-CoV-2 is more prone to immune escape. Presently, the significant variants of SARS-CoV-2 are emerging in due course of time with substantial mutations, having the immune escape property. Simultaneously, the vaccination drive against this virus is in progress worldwide. However, vaccine evasion has been noted by some of the newly emerging variants. Our review provides an overview of the emerging variants’ immune escape and vaccine escape ability. We have illustrated a broad view related to viral evolution, variants, and immune escape ability. Subsequently, different immune escape approaches of SARS-CoV-2 have been discussed. Different innate immune escape strategies adopted by the SARS-CoV-2 has been discussed like, IFN-I production dysregulation, cytokines related immune escape, immune escape associated with dendritic cell function and macrophages, natural killer cells and neutrophils related immune escape, PRRs associated immune evasion, and NLRP3 inflammasome associated immune evasion. Simultaneously we have discussed the significant mutations related to emerging variants and immune escape, such as mutations in the RBD region (N439K, L452R, E484K, N501Y, K444R) and other parts (D614G, P681R) of the S-glycoprotein. Mutations in other locations such as NSP1, NSP3, NSP6, ORF3, and ORF8 have also been discussed. Finally, we have illustrated the emerging variants’ partial vaccine (BioNTech/Pfizer mRNA/Oxford-AstraZeneca/BBIBP-CorV/ZF2001/Moderna mRNA/Johnson & Johnson vaccine) escape ability. This review will help gain in-depth knowledge related to immune escape, antibody escape, and partial vaccine escape ability of the virus and assist in controlling the current pandemic and prepare for the next.

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Section: P681rmentioning

confidence: 84%

A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations

et al. 2022

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“…Similarly, L452R mutation is reported in epsilon (B.1.427 and B.1.429), which is a variant of concern reported from California [17]. This mutation is reported to increase the rate of membrane fusion and thus lead to enhanced transmissibility [18]. The kappa variant thus epitomizes a conglomeration of key sequence variations that have previously been associated with important biological properties like enhanced viral attachment, cellular fusion and reduced neutralization with serum from convalescent individuals, vaccine recipients and monoclonal antibodies [19][20][21].…”

Section: Discussionmentioning

confidence: 89%

Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India

Singh

Malhotra

Biswas

et al. 2021

Genes

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India experienced a tragic second wave after the end of March 2021, which was far more massive than the first wave and was driven by the emergence of the novel delta variant (B.1.617.2) of the SARS-CoV-2 virus. In this study, we explored the local and national landscape of the viral variants in the period immediately preceding the second wave to gain insight into the mechanism of emergence of the delta variant and thus improve our understanding of the causation of the second wave. We randomly selected 20 SARS-CoV-2 positive samples diagnosed in our lab between 3 February and 8 March 2021 and subjected them to whole genome sequencing. Nine of the 20 sequenced genomes were classified as kappa variant (B.1.617.1). The phylogenetic analysis of pan-India SARS-CoV-2 genome sequences also suggested the gradual replacement of the α variant with the kappa variant during this period. This relative consolidation of the kappa variant was significant, since it shared 3 of the 4 signature mutations (L452R, E484Q and P681R) observed in the spike protein of delta variant and thus was likely to be the precursor in its evolution. This study demonstrates the predominance of the kappa variant in the period immediately prior to the second wave and underscores its role as the “bridging variant” between the α and delta variants that drove the first and second waves of COVID-19 in India, respectively.

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“…As these mutations are expected to destabilize the spike protein, they are expected to reduce antibody neutralization, which agrees with previous reports [ 24 , 27 ]. The mutation Q675H located in the Pre-Furin cleavage site in the spike protein, with the highest destabilizing ability, has appeared in Bangladesh in late 2020 [ 28 ]. However, some variants that have destabilized the protein with increased flexibility (e.g., E484K, K417 N, E484Q, Q675P, and Q675H) might impact the virus's ability to escape the antibodies neutralization by changing the antigenicity drift of the protein 3D structure; this is in agreement with a previous study [ [23] , [24] , [25] , [26] , [27] , [28] ].…”

Section: Discussionmentioning

confidence: 99%

Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines

Al-Zyoud

Haddad

2021

Biochimie

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The spike protein of SARS-CoV-2 plays a crucial role in binding with the human cell surface, which causes its pathogenicity. This study aimed to predict molecular dynamics change of emerging variants in the spike protein. In this study, several structural biology tools, such as SuperPose, were utilized to study spike protein structures' thermodynamics, superimposition, and the spike protein disulphide bonds. This questions the current vaccines efficacies that were based on the Nextstrain clade 19A that first documented in Wuhan and lacks any variants. The prediction results of this study have exhibited the stabilizing role of the globally dominant variant, the D614G; clade 20A, and other variants in addition to their role in increasing the flexibility of the spike protein of the virus. The SuperPose findings have revealed a conformational change impact of D614G in allowing the polybasic Furin cleavage site ( 682 RRAR↓S 686 ) to be closer to the receptor-binding domain (RBD) and hence more exposed to cleavage. The presence of D614G in any clade or subclade, such as 20A, B.1.1.7 (20I/501Y.V1) or Alpha, B.1.351 (20H/501Y.V2) or Beta, P.1 (20J/501Y.V3) or Gamma, B.1.617.2 (21A/478K.V1) or Delta, has increased its stability and flexibility and unified the superimposition among all clades which might impact the virus ability to escape the antibodies neutralization by changing the antigenicity drift of the protein three-dimensional (3D) structure from the wild type clade 19A; this is in agreement with previous study. In conclusion, a new design for the current vaccines to include at least the mutation D614G is immediately needed.

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Extensive genetic diversity with novel mutations in spike glycoprotein of severe acute respiratory syndrome coronavirus 2, Bangladesh in late 2020

Cited by 10 publications

References 27 publications

A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations

A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations

Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India

Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines

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