Introduction: Based on the 3D modeling of the SARS-CoV-2 spike-human ACE2 interactions we visualized the location of amino acids described as major mutation sites in the SARS-CoV-2 variants infecting humans, i.e., the S477N, E484K, and N501Y/T mutations known to characterize the Marseille-4 variant (France), the 20I/501Y.V1 variant (United Kingdom), and the 20H/501Y.V2 variant (South Africa) (Figure 8A, left panel).
Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI).
Introduction: The assay targets the RNA-dependent RNA polymerase (RdRp) gene, the S-protein N501Y and E484K mutations and HV69/70 deletion, as well as an endogenous internal control.
Introduction: Two subsequent variants of concern, B.1.351 (beta variant), first identified in South Africa, and P.1 (gamma variant), first identified in Brazil, were found to harbor the D614G and N501Y mutations, as well as 2 additional key mutations in the receptor binding domain (RBD), K417N/T and E484K, which increase binding affinity to the ACE2 receptor.
A Barcoded Flow Cytometric Assay to Explore the Antibody Responses Against SARS-CoV-2 Spike and Its Variants.
Result: RBD-specific IgG produced during the secondary response of the 12 vaccinated persons binds to a similar extent to Ramos cells carrying the WT, N501Y or
Result: For this, we introduced in the RBD-CD8 construct the N501Y and the E484K point mutations characteristic for the alpha and beta variant, respectively ( Figure 6A ).
Result: Interestingly, we found that, despite its lower expression, the N501Y mutant RBD-CD8 is bound better by ACE2-Ig than the WT RBD-CD8 construct, whereas Ramos cells expressing the G496I and E484K mutant RBD-CD8 constructs are less well bound by ACE2-Ig.
Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan.
PMID: 34631915
2021
Open forum infectious diseases
Introduction: Among the 9 mutations in the spike gene in this variant, there are 3 biologically important mutations: K417N, E484K, and N501Y.
Introduction: In addition, the B.1.351 and P.1 variants carry t
Discussion: However, the E484K mutation, which is found both in P.1 and B.1.351 but not in either D614G or B.1.1.7, has been reported to affect the binding of serum polyclonal neutralizing antibodies.
Discussion: On the other hand, because P.1 and B.1.351 have similar mutations in their RBD (including E484K, K417T/N, and N501Y), it might be thought that the neutralization of both variants would be affected similarly.
Mutational profile confers increased stability of SARS-CoV-2 spike protein in Brazilian isolates.
PMID: 34633892
2021
Journal of biomolecular structure & dynamics
Abstract: Mutations E484K, N501Y and K417N belong to several SARS-CoV-2 variants of concern such as Alpha, Beta, Gamma and Delta, and showed high incidence among Brazilian isolates.
SARS-CoV-2 monoclonal antibodies with therapeutic potential: Broad neutralizing activity and No evidence of antibody-dependent enhancement.
Figure: (a) Binding responses of anti-SARS-CoV-2 S protein mAbs, S1D2-hIgG1, STI-1499-LALA and 1741-LALA to the S1 fragment of the S protein from SARS-CoV-2 variants, including 2019-nCoV, B.1.1.7 (HV69-70 deletion, Y144 deletion, N501Y, A570D, D614G, P681H)-, B.1.351 ( Discussion: Further evidence shows receptor-binding domain (RBD) mutations E484K and combined K417N and N501Y mutations of SARS-CoV-2 B.1.351 and P.1 variants as vulnerabilities to multiple SARS-CoV-2 neutralizing mAbs engaging the RBD domain, and polyclonal Abs from convalescent sera or vaccine-induced immune sera.
Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro.
Method: To determine the binding EC50 of VNAR clones, high binding 96-well microplates (Greiner) were coated overnight at 4 C with 100 mul of S1, S1-RBD or HSA at 5 microg/ml and S1-RBD E484K and S1-RBD N501Y at 1 microg/ml.
Figure: ELISA was used to determine EC50 values for ACE2 binding to S1-RBD, S1-RBD N501Y, or S1-RBD E484K.
Figure: ELISA was used to determine EC50 values for individual VNAR-hFc antibodies to (A) S1, (B) S1-RBD, (C) S1-RBD N501Y, and (D) S1-RBD
SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response.
PMID: 34639178
2021
International journal of molecular sciences
Discussion: Importantly, N501Y and E484K were present, emerged frequently in earlier stages and have already been found in emerging variants, suggesting some predicting potential for possible new variants.
Discussion: One of the defining characteristics of this variant is the high number of mutations, particularly in the spike protein, with three mutations specific to the RBD (K417T, E484K and N501Y), that lead to a 19-fold increase in affinity compared to the Wuhan strain.
Discussion: Some of the mutations present in the optimized RBD are also present in new variants as critical mutations in variants of concern, appearing often and early in the mutagenesis process, particularly mutations PMID: 34642465
2021
Scientific reports
Discussion: 2A,B, Table S2), we considered all possible mutations actually reported at this position in circulating viral variants (i.e., E484A/D/G/K/Q/R/V), and found that all these amino acid variations should confer strong escaping ability to bamlanivimab.
Discussion: And this, in turn, support the view that vaccination elicits a natural infection-like antibody response, and that spike variants like E484K may spread as antigenic evolutions of SARS-CoV-2 to efficiently evade this response.
Discussion: As a conclusive remark concerning the available anti-SARS-CoV-2 vaccines, according to the report by Andreano and Rappuoli published on May 10, 2021 in Nature Medicine the efficacy of the FDA/EMA approved Ad26.COV2-S vaccine (now Janssen COVID-19 Vaccine) and the EMA appr
The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America.
3Introduction: As mentioned in Ref., RBD mutations such as E484K/A, Y489H, Q493K, and N501Y found in late-stage evolved S variants ""confer resistance to a common class of SARS-CoV-2 neutralizing antibodies"", which suggests the viral evolution is also regulated by vaccine-resistant mutations."
Introduction: Later on, we have provided a list of most likely vaccine escape RBD mutations with high frequency, including S494P, Q493L, K417N, F490S, F486L, R403K, E484K, L4
SARS_CoV_2 mutation literature information.
PMID: 
2021
Frontiers in microbiology
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