literature

SARS_CoV_2 mutation literature information.

Host Response to SARS-CoV2 and Emerging Variants in Pre-Existing Liver and Gastrointestinal Diseases.

PMID: 34760721 2021 Frontiers in cellular and infection microbiology

Introduction: This variant of B.1.1.7 lineage harbors receptor-binding domain (RBD) N501Y mutation and other mutations including 69/70 deletion, spike P681H, and ORF8 stop codon (Q27stop) mutation.The beta variant (20H/501Y.V2) of B.1.351 lineage harbors spike N501Y, E484K, and K417N/T mutations without 69/70 deletion and is predicted to have emerged in South Africa during October 2020 with potential of global spread.

Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation.

PMID: 34763050 2021 Infection, genetics and evolution

Result: The Gamma sequences generated herein presented the classical mutational signatures in spike glycoprotein L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I and V1176F, with some exceptions, as in the sample hCoV-19/Brazil/LMM53965 and hCoV-19/Brazil/LMM54004 that change a guanine for an adenine in 614 position (D614G D614A) and the hCoV-19/Brazil/LMM54029 that change a histidine for a glutamic acid in 655

CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern.

PMID: 34787487 2021 Microbiology spectrum

Abstract: Our results indicated that the CRISPR-Cas12a assay could readily detect the signature spike protein mutations (K417N/T, L452R/Q, T478K, E484K/Q, N501Y, and D614G) to distinguish alpha, beta, gamma, delta, kappa, lambda, and epsilon variants of SARS-CoV-2.

Table: K417T

Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak.

PMID: 34789293 2021 Virology journal

Table: K417T

Discussion: The Gamma-like-II lineage presents 15 of the 22 mutations of the Gamma variant, including the three main mutations in the RBD domain of the S protein: K417T, E484K and N501Y.

SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene.

PMID: 34796036 2021 Immune network

Introduction: Surprisingly, three K417T, E484K, and N501Y mutation sites in the critical RBD of S gene are identical to SARS-CoV-2 beta variant except K417 is substituted by T instead of N.

Table: K417T

Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants.

PMID: 34805715 2021 ACS omega

Introduction: For example, the P.1 lineage detected first in Brazil is characterized by several amino acid (AA) substitutions mostly located either in RBD or in NTD: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, and T1027I, which are shown to reduce neutralization by some antibodies.

Table: K417T

A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features.

PMID: 34806033 2021 Current research in structural biology

Result: For K417T in B.1.351 lineage, no significant alterations were observed.

Result: Further, for the characteristic RBD mutations across VoCs (K417 T/N, L452R, S

Discussion: studied the effect of five prevalent RBD mutations (K417N, K417T, N501Y, E484K, and S477N) on RBD-ACE2 interaction and suggested that the N501Y, E484K, and S477N mutations showed increased affinity towards ACE2 binding as compared to the wild type which might enhance transmission.

A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue.

PMID: 34829439 2021 Diagnostics (Basel, Switzerland)

Result: We explored the difference between binding to the beta and gamma RBDs, which differ only at K417 (beta, K417N; gamma, K417T).

Discussion: This is attributable to the K417N mutation, which alone reduces affinity 21.9-fold compared to a 13.8-fold reduction from the K417T change.

Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants.

PMID: 34848718 2021 Nature communications

Method: K417T, E484K, and N501Y) while the Kappa variant presents only two mutations.

Result: The same contact is more persistent in Alpha variant with freq ~ 0.9 and under mutations K417N and K417T in Beta and Gamma respectively, the contact frequency drops below 0.4, which correlates with the dramatic drop of the electrostatic contribution in the interfacial energy.

Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern.

PMID: 34856802 2021 Journal of chemical theory and computation

Conclusion: K417N/T mutations of Beta and Gamma appear to make the RBD-ACE2 interactions less strong compared to the Alpha variant.

Introduction: They investigated each specific mutation, N501Y

Method: From the WT RBD structure, each variant was modeled with the following mutations: Alpha (N501Y), Beta (K417N, E484K, N501Y), Gamma (K417T, E484K, N501Y), Epsilon (L452R), Kappa (L452R, E484Q), and Delta (L452R, T478K).

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