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<
Evaluation of a Rapid and Accessible Reverse Transcription-Quantitative PCR Approach for SARS-CoV-2 Variant of Concern Identification.
PMID: 35465708
2022
Journal of clinical microbiology
Abstract: We designed and analytically validated a two-reaction multiplex reverse transcription-quantitative PCR (RT-qPCR) assay targeting spike protein mutations L452R, E484K, and N501Y in reaction 1 and del69-70, K417N, and T478K in reaction 2.
Convergent Evolution of Multiple Mutations Improves the Viral Fitness of SARS-CoV-2 Variants by Balancing Positive and Negative Selection.
Abstract: N501Y increases receptor binding; however, it has decreased stability and expression.
Abstract: Triple mutant K417T/E484K/N501Y has increased receptor binding, escapes both Class 1 and Class 2 antibodies, and has similar stability and expression as that of the wild-type.
Abstract: We examined the physical mechanisms underlying the convergent evolution of three mutations K417T/E484K/N501Y by delineating the individual and collective effects of mutations on binding to angiotensin converting enzyme 2 receptor, immune escape from neutralizing antibodies, protein stability, and expression.
RBD-mRNA vaccine induces broadly neutralizing antibodies against Omicron and multiple other variants and protects mice from SARS-CoV-2 challenge.
Abstract: The RBD-mRNA-induced antibodies exerted moderate neutralization against authentic B.1.617.2 and B.1.1.529 variants, and pseudotyped B.1.351 and P.1 lineage variants containing K417N/T, E484K, and N501Y mutations, the B.1.617.2 lineage variant harboring L452R, T478K, and P681R mutations, and the B.1.1.529 lineage variant containing 38 mutations in the S protein.
Abstract: The vaccine induced durable antibodies that potently neutralized prototypic strain and B.1.1.7 lineage variant pseudoviruses containing N501Y or D614G mutations alone or in combination with a N439K mutation (B.1.258 lineage)
Binding Interactions between Receptor-Binding Domain of Spike Protein and Human Angiotensin Converting Enzyme-2 in Omicron Variant.
PMID: 35481766
2022
The journal of physical chemistry letters
Abstract: Other mutations, such as K417N, G446S, and Y505H, decrease the ACE2 binding, whereas S447N, Q493R, G496S, Q498R, and N501Y tend to increase it.
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
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.
Molecular Dynamics and MM-PBSA Analysis of the SARS-CoV-2 Gamma Variant in Complex with the hACE-2 Receptor.
Introduction: Additionally, the mutation N501Y exhibits a compensatory effect since it favors pi-pi interaction with the residue Y41.
Introduction: The alpha variant has three mutations of interest in the spike protein: (i) the N501Y mutation that corresponds to the receptor-binding motif (RBM); (ii) a 69/70 deletion in the receptor binding domain (RBD) that triggers a notable change in the conformation of the RBM; and (iii) the P681H mutation found near the furin S1/S2 cleavage site.
Introduction: The beta variant, also known as 20H/501Y.V2, was identified in South Africa and is characterized by carrying the K417N, E484K and N501Y mutations in the RBM of the
SARS_CoV_2 mutation literature information.
PMID: 
2022
Biomolecules
Browser Board
Co-occurred Entities
Filtrator
ViMRT