Abstract: We report that the Omicron brings an enhanced Method: In each variant, the Alpha includes N501Y mutation, Delta has L452R and T478K mutations, and Omicron contains 15 mutated amino acids, i.e., G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q483K/R, G496S, Q498R, N501Y, and Y505H (see also Figures 1B and 2D).
Divergent SARS-CoV-2 Omicron-reactive T and B cell responses in COVID-19 vaccine recipients.
Method: The delta variant contained the following spike changes: T19R, G142D, del156-157, R158G, A222V, L452R, T478K, D614G, P681R and D950N.
Method: The omicron variant contained the following spike mutations: A67VS, del69-70, T95I, G142-, del143-144, Y145D, del211, L212I, ins215EPE, G339D, S371L, S373P, S375F, K417N,
Mutations in the receptor-binding domain of human SARS CoV-2 spike protein increases its affinity to bind human ACE-2 receptor.
PMID: 35109768
2022
Journal of biomolecular structure & dynamics
Abstract: Here, we use the crystal structure of the RBD in complex with ACE-2 available in the public domain and analyse the 250 ns molecular dynamics (MD) simulations of wild-type and mutants; K417N, K417T, N440K, N501Y, L452R, T478K, E484K and S494P.
Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model.
Introduction: The RBD mutations found in Alpha (N501Y), Beta (K417N, E484K, and N501Y), Gamma (K417T, E484K, and N501Y), and Delta (L452R and T478K) are located in or closely adjacent to the ACE2-interacting surface where they have the potential to modulate ACE2 interaction or disrupt the binding of neutralizing mAbs.
Figure: (A-F) Neutralization assays performed against Victoria, Alpha (N501Y), Beta (K417N, E484K, and N501Y), Gamma (K417T, PMID: 35035981
2022
New microbes and new infections
Table: T478K
Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents.
Result: The Delta variant carries only L452R and T478K mutations in its RBD region, while the Omicron carries as much as fifteen RBD mutations of G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H.
Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift.
Introduction: As of March 2021, the 15 most commonly observed mutations in the RBD were as follows: V3
Figure: The 15 most commonly observed mutations in the RBD were as follows: N501Y, S477N, N439K, L452R, E484K, K417N, Y453F, S494P, A520S, N501T, T478K, V367F, S477R, P384L, and A522S, which were located at 13 sites in the RBD.
E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody.
PMID: 34915409
2022
International immunopharmacology
Introduction: Currently, there are four variants of concerns: Alpha variant (B.1.1.7; RBD mutations: N501Y, A570D), Beta (B.1.351; RBD mutations: K417N, E484K, and N501Y), Gamma (P.1, B.1.1.28.1; RBD mutations: K417N/T, E484K, and N501Y) and Delta (B.1.617.2; RBD mutations: L452R, T478K).
Omicron and Delta variant of SARS-CoV-2: A comparative computational study of spike protein.
Abstract: Based on docking studies, the Q493R, N501Y, S371L, S373P, S375F, Q498R, and T478K mutations contribute significantly to high binding affinity with human ACE2.
SARS_CoV_2 mutation literature information.
PMID: 
2022
bioRxiv
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