Abstract: We applied the primer set and wet-laboratory protocol to sequence 222 samples that were missing positions with key mutations K417N, E484K, and N501Y due to poor coverage after NGS sequencing.
Abstract: We successfully sequenced 153 samples of 222 (69 %) using Sanger sequencing and confirmed the occurrence of key beta variant mutations (K417N, E484K, N501Y) in the S genes of 142 of 153 (93 %) samples.
Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations?
Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method.
PMID: 35312321
2022
Journal of chemical information and modeling
Result: In N501Y, the difference of dispersion energy between the crystal structure of the wild type and the Omicron variant was calculated to be 4.3 kcal/mol, which is the biggest among the other residues due to the T-shaped pi-pi stacking interaction between Tyr41 in hACE2 and Tyr501 in the S protein of the Omicron variant (Figure S2).
Result: In the crystal structure, S375F, N440K, S477N, T478K, E484A, Q493R, G496S, Q498R, and N501Y interacted more strongly with the omicron variant than with the wild type (Table 2).
Result: The Table: N501Y
The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes.
Result: The SARS-CoV-2 Beta variant (B.1.351) spike, which we also examine here, also has a number of mutations, including K417N, E484K, and N501Y mutations in the RBD (Fig 1B).
SARS-CoV-2 Omicron variant: Immune escape and vaccine development.
Introduction: For instance, the K417N and N501Y mutations were known to confer protection against a number of mAbs.
Introduction: Furthermore, consistent with the observations highlighted above, the Q498R substitution may act synergistically with the existing N501Y substitution to increase the affinity of the spike protein to ACE2.
Introduction: Interestingly, the presence of the K417N mutation did not affect spike-ACE2 binding affinity but produced positive cooperativity with E484K/N501Y.
Introduction: One example is the N501Y mutation, shared by Alpha, Beta, and Gamma variants, which enhances the binding of
Omicron Variant of SARS-CoV-2 Virus: In Silico Evaluation of the Possible Impact on People Affected by Diabetes Mellitus.
Introduction: Some of these mutations, such as Q498R and N501Y, have already proven to lead to an increased affinity with ACE2 in respect to WT-Spike.
Discussion: This variation, together with several mutations on Spike-RBD that were linked to an increased affinity for ACE2 (such as S477N, Q498R, and N501Y), is predicted to contribute to an increase in the interactivity between Omicron-Spike-RBD and ACE2 in a hyperglycemic environment.
First detection of SARS-CoV-2 lineage A.27 in Sardinia, Italy.
PMID: 35324468
2022
Annali dell'Istituto superiore di sanita
Abstract: Among the key mutations identified in the spike protein, the N501Y and the L452R deserve attention as considered likely vaccine escape mutations.
Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds.
Result: Finally, 1/32 sequence was the Omicron strain, with the following mutations in the RBD domain: T22882G (N440K), G22898A (G446S), G22992A (S477N), C22995A (T478K), A23013C (E484A), A23040G (Q493R), G23048A (G496S), A23055G (Q498R), A23063T (N501Y), T23075C ( PMID: 35336952
2022
Viruses
Result: N501Y is present in the Alpha, Beta, and Gamma variants, and this substitution increases binding affinity to angiotensin-converting enzyme receptor 2 (ACE2), playing an essential role in the higher rate of transmission of SARS-CoV-2 variants.
Result: Figure 3 shows the most frequent amino acid substitutions in the RBD (G339D, R346K, K417N, S371L, S373P, S375F, N440K, Q498R, and N501Y).
Result: On the other hand, the prevalence of eleven substitutions (S371L, S373P, S375F,
ViMRT
SARS_CoV_2 mutation literature information.
PMID: 
2022
Microbial genomics
