Role of the Microbiome in the Pathogenesis of COVID-19.
PMID: 35433495
2022
Frontiers in cellular and infection microbiology
Conclusion: The neutralization resistance occurred due to E484K and N501Y mutations in the RBD of the spike.
Introduction: These were the N501Y (asparagine to tyrosine substitution at position 501 in the S gene) and the 69-70del (a deletion of 6 bases coding for histidine and valine at positions 69 and 70 in the S gene) mutations.
Introduction: This variant has the same mutation N501Y like the UK variant; however, the two variants are phylogenetically not related 4 .
Table: N501Y
Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD.
Result: The RBD contains three mutations, which are Y449H, E484K, and N501
Result: The B.1.640.1 variant contains 22 mutations in spike protein, of which the RBD contains five mutations of R346S, N394S, Y449N, F490R, and N501Y.
Discussion: The immunogenicity of Beta, Gamma, and Mu were similar, probably because these three immunogens all contained E484K and N501Y mutations (Figure S1).
Discussion: The neutralizing activity of mAb JS016 was reduced due to the N501Y mutation in the variants.
Characteristic analysis of Omicron-included SARS-CoV-2 variants of concern.
Result: The scores of E484K and N501Y are also relatively close, indicating that these mutations do not affect the epitope of the spike protein of the Beta strain (Figure 2E).
Discussion:
Discussion: In the Alpha and Omicron strains, two key deletions, H60V70, are on the epitope, which can affect the immune escape of the S protein (Figure 4F), whereas N501Y and D614G have almost no effect on the antigen score, and the P681 mutation slightly reduces the epitope score and may have a certain impact.
Discussion: In the Omicron variant, there are some consistent RBD mutations with previously focused variants (K417N, T478K, and N501Y).
Mutational Effect of Some Major COVID-19 Variants on Binding of the S Protein to ACE2.
Abstract: Our calculations show that five major mutations (N501Y, E484K, L452R, T478K and K417N), first reported in Alpha, Beta, Gamma an
Introduction: As shown in Table 1, these three variants have one point in common:that is, the N501Y mutation, which was reported to accelerate the spread of virus through stronger binding with ACE2.
Introduction: We first focus on five specific mutations (N501Y, E484K, L452R, T478K and K417N) that were found in Alpha, Beta Gamma and Delta variants, and these mutations are all located on the RBDs of the SARS-CoV-2/ACE2 complex.
Comparative Evaluation of Six SARS-CoV-2 Real-Time RT-PCR Diagnostic Approaches Shows Substantial Genomic Variant-Dependent Intra- and Inter-Test Variability, Poor Interchangeability of Cycle Threshold and Complementary Turn-Around Times.
Discussion: In addition, variant B.1.258.17 as the main lineage during the second wave, variant A.27 as a rare variant, with mutation N501Y, and variant B.1 (with D614G) as the first main lineage, which caused a substantial part of the first wave of infections in Europe, were included.
Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations.
PMID: 35457196
2022
International journal of molecular sciences
Result: Although the destabilization changes in these positions are less dramatic than for the N501Y position, we found that the reverse mutations R493Q, S496G and R498Q can result in DeltaDeltaG = 0.7-1.2 kcal/mol (Figure 4E,F).
Result: In the Omicron RBD-ACE2 complex, a considerable number of the binding interfaces (G446, Y449, F486, Y489, G496S, Q498R, T500, N501Y and Y505H) become stabilized to make strong specific interactions with ACE2 (Figure 2A).
Result: Instructively, the N501 position does not belong to strong binding energy hotspots in the native S-RBD and S<
Longitudinal Analysis of Neutralizing Potency against SARS-CoV-2 in the Recovered Patients after Treatment with or without Favipiravir.
Abstract: These subjects participated in the longitudinal (>6 months) analysis of (i) SARS-CoV-2 spike protein's receptor-binding domain IgG, (ii) virus neutralization assay using authentic virus, and (iii) neutralization potency against original (WT) SARS-CoV-2 and cross-neutralization against B.1.351 (beta) variant carrying triple mutations of K417N, E484K, and N501Y.
Result: The sera collected from 34 patients were further assessed to quantify antibodies against SARS-CoV-2 variant of B.1.351 (beta) carrying triple mutations of K417N, E484K, and N501Y).
Highly Thermotolerant SARS-CoV-2 Vaccine Elicits Neutralising Antibodies against Delta and Omicron in Mice.
Method: mRBD1-3.2-beta was generated in the background of stabilised mRBD1-3.2 (A348P, Y365W and P527L), and it has three important mutations (K417N, E484K and N501Y) present in the RBD of the Beta (B.1.351) VOC.
Result: Vaccine 3 is matched to Beta; however, this VOC only shares N501Y and K417N mutations with Omicron.
Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity.
Result: However, monitoring infectivity levels of pseudoviruses that carried the double S477N/N501Y exhibited a x12-fold increase in viral infectivity relative to wild type or single S477N pseudoviruses (Figure 5B).
Result: Moreover, pseudoviruses that carried double-P681H/N501Y, or A701V/N501Y mutations within their wild-type spike were also tested and exhibited similar neutralization potential as the single mutated N501Y pseudoviruses, or wild-type SARS-CoV-2 pseudoviruses (Figure 2A).
Result: Moreover, pseudoviruses that carried the A7101V/N501Y or P681H/N501Y
Decreased and Heterogeneous Neutralizing Antibody Responses Against RBD of SARS-CoV-2 Variants After mRNA Vaccination.
Method: Primers used for the construction of the RBD-mFc proteins for the different variants (Alpha RBD-mFc, containing mutation N501Y; Gamma RBD-mFc containing mutations K417T, E484K, and N501Y; Delta RBD-mFc containing mutations L452R and T478K); Epsilon RBD-mFc containing mutation L452R; and Kappa RBD-mFc containing mutations L452R and E484Q), were obtained from Sigma-Aldrich and are shown in Supplementary Table 2 .
SARS_CoV_2 mutation literature information.
PMID: 
2022
Frontiers in cellular and infection microbiology
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