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.
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
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
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
Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2.
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.
Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing.
Introduction: The Gamma variants described in Brazil belonging to the lineage P.1 clade 20J also have the E484K mutation in addition to K417T and N501Y mutations in their RBD.
A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants.
Introduction: Most class I mAbs were largely disrupted by the K417N/T mutation and class II mAbs by the E484K mutation.
Introduction: The Beta and Gamma variants each has three mutation sites in common within the RBD region:K417N/T, E484K, and N501Y:which change their antigenic profiles.
Result: In contrast, P36-1B7, like the class I mAb CB6, was substantially impacted by the SARS-CoV-2 Alpha, Beta, and Gamma variants, largely due to K417N/T and N501Y mutations.
Figure: (A) The epitope of P36-5D2 (purple) is highlighted on the surface of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RBD
Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data.
Result: Furthermore, for Cq over 25 no SARS-CoV-2 variant (K417N/T, E484K, and N501Y) sample was detected by RAT.
Result: Interestingly, from the three SARS-CoV-2 (K417N/T, E484K, and N501Y) positive samples for RAT, two of them presented a band of low intensity (Table 2) compared to SARS-CoV-2 samples with no mutations identified, which present a high-intensity band in the range 20>=Cq <25 (Table 1).
Result: When we evaluated these NPSs containing SARS-CoV-2 variants, we observed that the sensitivity of RAT decreased in the variants that carry K417N/T and E484K amino acid substitutions, even in samples with the lowest ranges of Cq (20 <= Cq <25).
Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka.
Introduction: Viruses of the lineage B.1 have acquired several other amino acid replacements in the Receptor Binding Domain of the Spike protein - specifically in the lineages which have been designated as VOCs, namely -B.1.1.7 (N501Y), B.1.351 (N501Y, E484K, K417T) and P.1 from the lineage B.1.1.28 (N501Y, E484K, K417T).
SARS_CoV_2 mutation literature information.
PMID: 
2021
PloS one
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