Discussion: Spike variants such as D614G and N501Y, contained in the 20H/501Y.V2 and 20I/501Y.V1 clades, may lead to changes in viral antigenicity that are harmful to monoclonal antibody therapies and vaccine protection, thereby mediating potential escape from vaccine response.
Dieckol and Its Derivatives as Potential Inhibitors of SARS-CoV-2 Spike Protein (UK Strain: VUI 202012/01): A Computational Study.
Introduction: Of note, Tyr453Phe and Asn501Tyr mutations are located in the receptor-binding domain (RBD) of SARS-CoV-2.
Introduction: The new variant is characterized by many mutations such as Delta69-70, Delta144, Tyr453Phe, Asn501Tyr, Ala570Asp, Asp614Gly, Phe681His, Thr716Ile,
Method: A model of UK SARS-CoV-2 Spike protein RBD was generated by inserting Tyr453Phe and Asn501Tyr mutations in the Spike protein RBD using PyMol.
Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern.
Result: However, the mutation N501Y increases molecular interactions in all VOC, while the residue Y501 (Tyr501) forms a H-bond with K353 (Lys353) on hACE2 (H-bond lengths ranging from 2.82 to 2.94 A).
Result: In addition, the UK-VOC contains several nonsynonymous mutations that cause seven aa substitutions at positions N501Y, A570D, D614G, P681H, T716I, S982A, D1118H in S-protein, in which N501Y mutation occurs in the key residue of RBD.
Result: Several mutations can be seen in the RBD of VOC, including K417N/T,
SARS-CoV-2 mutations: the biological trackway towards viral fitness.
Introduction: N501Y falls within the RBD and had been shown to enhance the binding affinity of S protein with human ACE2.
Introduction: VUI202012/01 had eight mutations in S protein of which N501Y, P681H, Delta69 and Delta70 have potential implications on viral infectivity.
Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K.
Introduction: 11 Virtually all variants of concern contain mutations in the SARS-CoV-2 Spike protein, such as variant B.1.351 (Spike mutations K417N, E484K, N501Y, D614G, and A701V) and variants B.1.427/B.1.429 (Spike mutations S13I, W152C, L452R, and D614G), and many of these reside on the receptor-binding domain (RBD), a region located between residues 350-550 of Spike and directly binding to the human ACE2.
Introduction: 8 , 14 , 15 , 16 A recently published clinical study 17 has shown also a dec
Structural Consequences of Variation in SARS-CoV-2 B.1.1.7.
PMID: 33969357
2021
Journal of cellular immunology
Abstract: N501Y increased affinity between the spike protein and ACE2.
Result: N50
Result: Although N501Y has the potential to influence neutralizing antibody binding, this semiconservative difference is located at the edge of the ACE2/spike protein interface, therefore not expected to dramatically alter neutralizing antibody responses.
Result: Collectively, these data suggest that: 1) the UK variant B.1.1.7 exhibits a change that enhances affinity for the coronavirus receptor ACE2 (N501Y), and 2) mutations may enhance dynamic virus fusion mechanisms by reducing intermolecular stability of spike protein subunits (A570D, D614G, S982A).
A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern.
PMID: 33975021
2021
Infection, genetics and evolution
Abstract: Here we propose a rapid and accessible protocol based on Sanger sequencing of a single PCR fragment that is able to identify and discriminate all SARS-CoV-2 variants of concern (VOCs) identified so far, according to each characteristic mutational profile at the Spike-RBD region (K417N/T, E484K, N501Y, A570D).
Introduction: Specific mutations, such as the N501Y and the E484K, in the receptor binding domain (RBD) of the Spike protein are recurrent across VOCs.
Introduction: The K417, E484 and N501Y mutations were identified in the samples assigned
Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines?
PMID: 33975397
2021
Journal of Korean medical science
Conclusion: Unfortunately, the mutation frequency of the S protein is very high, and some mutations (such as E484K, N501Y, and K417N) affect the transmission and neutralization of the SARS-CoV-2 virus.
Introduction: The SARS-CoV-2 B.1.351 variant in South Africa has eight mutations involving the S protein (L18F, D80A, D215G, R246I, K417N, E484K, N501Y, and A701V).
Introduction: The SARS-CoV-2 P.1 variant in Brazil harbors three S protein mutations E484K,
SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes.
Result: N501Y arose, apparently independently, in the B.1.153 lineage, which rapidly rose in frequency in South Africa and also includes spike-protein substitutions E484K and K417N, which are thought to decrease binding of antibodies from monoclonal antibody cocktails or from immune re
Result: However, as noted above, ORF8 shows strong evolutionary evidence of protein-coding function across this coronavirus species and experimental evidence of expression in SARS-CoV-2, together indicating that ORF8 loss would be expected to have a fitness cost, which is only tolerated due to hitchhiking with the highly advantageous N501Y spike protein substitution and possibly additional selected variants in the haplotype.
Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein.
Abstract: Spike protein mutations E484K and N501Y carried by SARS-CoV-2 variants have been associated with concerning changes of the virus, including resistance to neutralizing antibodies and increased transmissibility.
Abstract: In response to the unmet need for a fast and efficient screening tool, we developed a single-tube duplex molecular assay for rapid and simultaneous identification of E484K and N501Y mutations from nasopharyngeal swab (NS) samples within 2.5 h from sample preparation to report.
Abstract: Our data revealed dramatic increases in the frequencies of both E484K and N501Y over time, underscoring the need for continuous epidemiological monitoring.
SARS_CoV_2 mutation literature information.
PMID: 
2021
Biomedicines
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