Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7.
Introduction: A number of substitutions in S have been associated with immune escape (e.g., E484K, K417N), or increased binding to the ACE-2 receptor (e.g., N501Y).
Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern.
Abstract: However, mutations at the residue K417N/T are shown to reduce the binding affinity.
Abstract: Notable nonsynonymous mutations in RBD of VOC include the E484K and K417N/T that can be seen in South African and Brazilian variants, and N501Y and D614G that can be seen in all VOC.
Result: Several mutations can be seen in the RBD of VOC, including K417N/T, E484K and N501Y, while two later mutations are located in contact residue responsible to directly bind to hACE2 (Figure 2).
Result: The SA-VOC has seven aa substitutions in the S-protein, including
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.
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).
Table: K417N
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
Abstract: Furthermore, mutations such as N501Y, E484K, and K417N in the S protein may affect viral fitness and transmissibility.
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, E48
SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes.
Abstract: Evolutionary histories of residues disrupted by spike-protein substitutions D614G, N501Y, E484K, and K417N/T provide clues about their biology, and we catalog likely-functional co-inherited mutations.
Result: N501Y arose, apparently independently, in the B.1.153 lineage, which rapidly rose in frequency in South Africa and also includes Discussion: Sarbecovirus evolutionary histories provided clues to the biology of spike-gene mutations D614G, N501Y, E484K, and K417N/T and allowed us to catalog co-inherited mutations likely to have functional consequences.
Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility.
Result: In contrast to E484K and N501Y, K417T alone appears not favored for receptor recognition, and this is reflected in reduced affinities for K417T/N501Y and K417T/E484K combinations, which are not observed together in sequenced viral genomes; K417N has similar characteristics (not shown).
Result: In vitro evolution of optimized Spike RBD repeatedly recovered S477N, E484K and N501Y mutations but not K417N/T.
Result: Mutants E484K/R exhi
Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries.
Conclusion: More specifically, we found that mutations N501Y, E484K, and K417N in the United Kingdom (UK), South Africa, or Brazil variants, L452R and E484Q in the India, as well as mutations N439K, S477N, S477R, and N501T are all associated with the enhancement of the BFE of the S protein and ACE2, confirming the earlier speculation.
Conclusion: We report that rapidly growing mutations S494P, Q493L, K417N, F486L, F490S, R403K,
Novel SARS-CoV-2 variants: the pandemics within the pandemic.
PMID: 34015535
2021
Clinical microbiology and infection
Table: K417N
Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil.
Discussion: Until mid-December 2020, 157 genomes have this mutation globally, 114 (72.6%) isolated from South Africa, where a new lineage (B.1.351 or 501Y.V2) characterized by three RBD mutations (K417N, E484K and N501Y) recently emerged.
SARS_CoV_2 mutation literature information.
PMID: 
2021
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