Method: The following variant spikes were made (SA, Alpha and mink) (all mutations listed with reference to the NCBI sequence YP_009724390.1): 2P Alpha (Delta69-70, Delta144, N501Y, A570D, D614G, P681H, T716A, S982A, D1118H, and K986P, V987P), FUR2P Alpha (Delta69-70, Delta144, N501Y, A570D, D614G, T716A, S982A, D1118H, and R682S, R685S, K
Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites.
Method: SARS-CoV-2 TaqMan Assays for S substitutions K417T, E484K, E484Q, and L452R were performed per manufacturer's instructions (Thermo Fisher) with 4 muL of template.
Result: Amplification failure was expected and occurred for strains lacking both reference and mutation sequences at the locus (e.g., B.1.351 lacks both alleles at K417T, B.1.351 and P.1 lack both alleles at E484Q, and B.1.617.1 lacks both alleles at E484K) which indicates high specificity of all assays performed on synthetic RNA.
Result: Furthermore, of the 96 replicates that produced an inconclusive result, 74 were due to the presence of an alternate allele: 70 replicates containing E484K (B.1.351 an
Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination.
Discussion: Amino acid changes in spike proteins of variants contribute to immune evasion, and it has been suggested that N501Y is associated with increased infectivity, whereas L452R, T478K, and E484K with K417N reduce the interaction of neutralizing antibodies with RBD.
Discussion: However, Eta with slightly reduced neutralization results has solely an E484K substitution, indicating that the E484K substitution alone is not able to substantially decrease the neutralization efficacy of vaccine-induced antibodies.
Discussion: Similar findings have been observed by others, and especially amino acid change E484K in Beta has been linked
Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q.
Introduction: Another variant, B.1.351 (Mwenda et al.) and P.1 variant (Francisco et al.) carries 9 and 11 spike protein mutations, respectively, including 3 mutations in the receptor-binding domain (RBD), K417N/T, E484K, and N501Y.
Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion.
Introduction: Also, the E484Q mutation is similar to the E484K mutation found in the B.1.351 variant, which exhibited reduced neutralization by convalescent-phase sera or monoclonal antibodies.
Introduction: B.1.618 harbors Delta145-146 (deletion of the 145th and 146th residues) and an E484K mutation in the NTD and RBD, respectively.
Introduction: For the Kappa and Delta variants, this is the first time that L452R and E484Q (Kappa)/T478K (Delta) mutations have been found to coexist and the first time that P681R has been observed; for B.1.618, this is the first time the combination of Delta145-146 in the NTD domain and E484K has been observed.
Introduction: In
Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm.
PMID: 35266951
2022
Genetics and molecular biology
Introduction: Currently, the WHO has identified the Gamma lineage (B.1.1.28.1, P.1 or Gamma; Nextstrain clade 20J/V3) with the following key S mutations: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, and V1176F.
Introduction: The WHO and other reports identified several key SARS-CoV-2
Result: Notably, in our analysis, a number of these sites (e.g., E484K) did not exhibit evidence of positive selection.
Table: E484K
A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay.
PMID: 35271889
2022
Journal of virological methods
Method: Finally, a 598 PCR product containing L452R, E484K/Q, T478K, and D614G were synthesized, and then sequencing was done.
Method: Samples with the positive result for del69-70, E484K, E484Q, D614G, and Table: E484K
Figure: C) Amplification curves E484K using E484K primers and probes.
Figure: Schematic of the mutations del69-70, E484K, E484Q, D614G, L452R, and T478K that were selected for dominant variant screening.b.
A SARS-CoV-2 Wuhan spike virosome vaccine induces superior neutralization breadth compared to one using the Beta spike.
Method: Pre-fusion spike protein ectodomain DNA constructs were designed containing the following mutations compared to the Wuhan variant (Wuhan Hu-1; GenBank: MN908947.3): deletion of H69, V70 and Y144, N501Y, A570D, D614G, P681H, T716I, S982A and D1118H in Alpha; L18F, D80A, D215G, L242H, R246I, K417N, E484K, N501Y, D614G and A701V in Beta;
SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines.
Introduction: And cilgavimab had lower activity against N501Y+D614G mutants, including B.1.429 (carrying L452R), B.1.617.2 (carrying L452R + T478K) and B.1.351 (carrying K417N + E484K + N501Y).
Introduction: E484 substitutions have been identified in a number of VOCs, including B.1.351 (E484K), P.1 (E484K), B.1.617.2 (E484K/E484Q) and B.1.1.529 (E484A) (https://covariants.org/variants/S.E484).
Introduction: Examples include the N501Y, S477N, PMID: 35279013
2022
Biomedicine & pharmacotherapy
Discussion: Although E484 is located outside of ACE2 binding area, E484K mutation can abolish the binding of RBD to some antibodies, including bamlanivimab.
Discussion: Beta variant contains nine mutations in SARS-CoV-2 spike protein: D614G, Delta242-Delta244, R246I, K417N, E484K, N501Y, and A701V.
Discussion: However, 50 mug/mL glycyrrhizic acid did not affect the binding between ACE2 and RBD with K417N-E484K-N501Y mutation.
Discussion: In our results, GB-1 has higher inhibitory ability in the variant with
ViMRT
SARS_CoV_2 mutation literature information.
PMID: 
2022
Nature communications
