literature

SARS_CoV_2 mutation literature information.

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.

Divergent SARS-CoV-2 Omicron-reactive T and B cell responses in COVID-19 vaccine recipients.

PMID: 35113647 2022 Science immunology

Method: The beta variant contained the following spike changes: L18F, D80A, D215G, del241-243, K417N, E484K, N501Y, D614G, and A701V.

Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display.

PMID: 35114110 2022 Cell reports

Abstract: Further, we engineer a potent ACE2-blocking nAb to sustain binding to S RBD with the E484K and L452R substitutions found in multiple SARS-CoV-2 variants.

Discussion: Further, while we determined it was outside the scope of the current paper, we did not generate/analyze crystal structures of an escape variant such as RBD-E484K in complex with antibodies N-612-017-01/03 in comparison with N-612-017.

Discussion: Our N-612-017 antibody is a class 2 RBD binder similar to bamlanivimab that also displays a loss of activity in the presence of the E484K mutation.

Breadth of SARS-CoV-2 Neutralization and Protection Induced by a Nanoparticle Vaccine.

PMID: 35118474 2022 bioRxiv

Method: D614G spike mutation: D614G; Alpha (B.1.1.7) spike mutations: Delta69-70, Delta144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H; Beta (B.1.351) spike mutations: L18F, D80A, D215G, Delta242-244, R246I, K417N, E484K, N501Y, D614G, A701V; Delta (B.1.61

Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia.

PMID: 35213571 2022 PloS one

Result: Taken together, the missense mutations, Discussion: Higher infectivity of the SARS-CoV-2 variants is associated with increased in binding affinity between spike protein and ACE2 due to K417N, E484K, N439K and N501Y mutations in the RBD of the spike protein.

Discussion: While N501Y mutation alone enhanced spike RBD-ACE2 affinity, combination of K417N, E484K and N501Y mutations in B.1.351 lineage resulted in noticeable conformational changes in RBD when bound to ACE2.

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.

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.

PMID: 35266815 2022 mBio

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.

Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q.

PMID: 35265451 2022 3 Biotech

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.

Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination.

PMID: 35262410 2022 Microbiology spectrum

Result: including N501Y in both Alpha and Beta, E484K in Eta and Beta, K417N in Beta, and L452R and T478K only in Delta.

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

PMID: 35262087 2022 medRxiv

Abstract: The SNP assays (K417T, E484K, E484Q,

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.

Discussion: The accuracies of K417T, E484K, E484Q, and L452R assays were >= 96.4% (Table 3).

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