Method: SARS-CoV-2 pseudotyped lentiviruses were prepared by co-transfecting the HEK293T cell line with either the SARS-CoV-2 ancestral variant spike (D614G), the Beta spike (L18F, D80A, D215G, K417N, E484K, N501Y, D614G, A701V, 242-244 del) or the Delta spike (T19R, R158G L452R, T478K, D614G, P681R, D950N, 156-157 del) plasmids in co
Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617.
Introduction: For example, T478K aa change in the receptor-binding domain (RBD) and 156-157 deletions in the N-terminal domain (NTD) of the S protein are unique to B.1.617.2, while E154K and Q1071H substitutions exist only in the B.1.617.1 sublineage.
Result: Of these eight mutated sites, seven were non-synonymous mutations (T19R, I95T, G142D, K154E, T478K, Q484E, and D950N), and one was a synonymous mutation (D333).
Result: The aa substitutions with occurrence frequencies >1% were V382L,
Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein.
Result: As mentioned earlier, L452R and T478K are signature mutations in the delta variant.
Result: During this period, N501Y, L452R and T478K mutations increased by 15.39, 23.06 and 26.75% points, respectively, while E484K, S477N, K417T and S494P mutations decreased by 1.35, 3.09, 0.37 and 0.88% points, respectively.
Result: Further, we observed a considerable prevalence of other adaptive mutations in the RBD, namely L452R, T478K, E484K, S477N, K417T,
Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach.
Figure: (B) Protein models of S protein containing T478I/R/K or E484K/Q mutations together with D614G double mutations were superposed onto the prototype.
Figure: Note the T478R/K + D614G and E484Q + D614G double mutants are >93% identitical to the prototype, while the S1-RBD domain of T478I + D614G and E484K + D614G double mutants were not aligned with the prototype.
Discussion: However, T478R/K (polar to positive-charge residue) and
Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach.
PMID: 34720581
2021
Bioinformatics and biology insights
Result: We also analyzed the effect of 27 missense variants of SARS-CoV-2 spike protein (RBD) on the binding interaction of spike protein with ACE2 and observed that L452Q, T478K, L455F, F456L, S459F, A475V, N439K, L452R, T470N, E484D, E484A, E484K, E484Q, F486L, S494P, S494L, N501T, PMID: 34723159
2021
iScience
Abstract: Highly transmissible SARS-CoV-2 variants identified in India and designated B.1.617, Kappa (B.1.617.1), Delta (B.1.617.2), B.1.618, and B.1.36.29 contain spike mutations L452R, T478K, E484K, E484Q, and N440K located within the spike receptor-binding domain and thus could contribute to increased transmissibility and potentially allow re-infection or cause resistance to vaccine-elicited antibody.
Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan.
A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants.
PMID: 34732694
2021
Signal transduction and targeted therapy
Result: We investigated several RBD variants within publicly available SARS-CoV-2 sequences in the Global Initiative on Sharing All Influenza Data (GISAID) and all of the individual RBD mutants (N501Y, E484K, E484Q, K417N, K417T, L452R, L452Q, T478K) found in dominant VOCs (B.1.1.7, Alpha; B.1.352, Beta; P.1, Gamma; B.1.617.2, Delta; B.1.427/B.1.429, Epsilon) for n3113.1 binding.
Method: They are: S.K417T.AAG.ACG, S.D614G.GAT.GGT, S.E484K.GAA.AAA, S.E484Q.GAA.CA
Result: Out of nine samples, five were B.1.617.2 (Delta) and concordant with sequencing showing mutation in D614G, L452R, P681R, and T478K, two samples were B.1.1.7 (Alpha) showing mutation in D614G, N501Y, delH69V70, Q27stop, and two were B.1.526 (Iota) showing mutation in L452R and D614G (Supplementary Material S5).
Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations.
Discussion: On the other hand, for MT2, MT3, and RBD versions involving mutations K417N, L452R, E484K, T478K, and N501Y, the binding energy increased compared to the WT.
Discussion: We found that mutation N501Y marginally enhanced the binding energy between RBD and ACE2, while mutations MT2 (E484K/
Discussion: reported that the binding between SARS2 and ACE2 increases when the following mutations K417N, E484K, L452R, T478K, and N501Y are present, in good agreement with our findings.
SARS_CoV_2 mutation literature information.
PMID: 
2021
Cell host & microbe
Browser Board
Co-occurred Entities
Filtrator
ViMRT