Discussion: To further differentiate Alpha, Beta, Gamma, and Mu, other mutation sites in the Spike protein like 69-70 deletion or 144 deletion, 242-244 deletion or K417N, R190S or K417T, T95I or R346K can be detected respectively.
The Development of SARS-CoV-2 Variants: The Gene Makes the Disease.
PMID: 34940505
2021
Journal of developmental biology
Abstract: Some concerning mutations associated with an impact on viral fitness have been described in the Spike protein, such as D614G, N501Y, E484K, K417N/T, L452R, and P681R, among others.
Introduction: Close to them within the RBD, K417N, and K417T mutations have been repeatedly described to protect against binding to certain monoclonal antibodies.
Introduction: In fact, it has been proposed that K417N could provide a slightly improved ACE2 binding compared to K417T.
Introduction: Nevertheless, both K417N and
Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants.
Introduction: The Gamma P.1 variant encodes an S protein with 12 mutations (L18F, T20N, P26S, D138Y, R190S, K417N/T, E484K, N501Y, D614G, H655Y, T1027I, and V1176F), two of which are in the RBD (E484K, and N501Y).
Discussion: For the Alpha (B.1.1.7) and Beta (B.1.351) variants, the del 69-70, del 144, and del 242-244 deletions in NTD and the K417N/T, E484K
Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding.
Introduction: The one RBD mutation occurring outside of the RBM, K417N/T, additionally exhibits ambiguity in mutation, with the P.1 strain mutated to threonine (K417T) and the B.1.351 strain mutated to asparagine (K417N) (Figure 1B).
Discussion: Although there are many factors governing viral evolution, these results suggest that the independent evolution of L452R-bearing spikes and N501Y-, K417N/T-, and E484K-bearing spikes may be explained by a lack of synergistic increase in ACE2 binding upon combination of these mutations.
Discussion: Consistent with this hypothesis, analysis of deposited sp
Development of an efficient Sanger sequencing-based assay for detecting SARS-CoV-2 spike mutations.
Abstract: Here, we developed five SARS-CoV-2 spike gene primer pairs (5-SSG primer assay; 69S, 144S, 417S, 484S, and 570S) and verified their ability to detect nine key spike mutations (DeltaH69/V70, T95I, G142D, DeltaY144, K417T/N, L452R, E484K/Q, N501Y, and H655Y) using a Sanger sequencing-based assay.
Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants.
Introduction: Subsequent reports have demonstrated that increased transmissibility and immune escape are linked to these lineages, which are defined by spike receptor binding domain (RBD) mutations, including N501Y, K417N/T, L452R, and E484K.
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.
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.
Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants.
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
SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene.
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.
SARS_CoV_2 mutation literature information.
PMID: 
2021
PloS one
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