SARS_CoV_2 mutation literature information.


  Emerging vaccine-breakthrough SARS-CoV-2 variants.
 PMID: 34518803       2021       ArXiv
Introduction: By analyzing the frequency, binding free energy (BFE) changes, and antibody disruption counts of RBD co-mutations, we reveal that nine RBD co-mutation sets, namely [L452R, T478K], [L452Q, F490S], [E484K, N501Y], [F490S, N501Y], [S494P, N501Y], [K417T, E484K, N501Y], [K417N, L452R, T478K], [K417N,


  Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis.
 PMID: 34526698       2021       Nature medicine
Method: SARS-CoV-2 neutralizing antibodies were quantified using lentivirus particles that incorporate SARS-CoV-2 S protein (Wuhan-Hu-1 isolate mutated to contain D614G) or the B.1.351 variant S protein (L18F-D80A-D215G- L242- A243- L244-K417N-E484K-N501Y-D614G-A701V) on their surface and express firefly luciferase reporter gene for quantitative measurements of infection by relative luminescence units (RLUs) as described.


  A bioluminescent and homogeneous SARS-CoV-2 spike RBD and hACE2 interaction assay for antiviral screening and monitoring patient neutralizing antibody levels.
 PMID: 34531417       2021       Scientific reports
Method: The following proteins were purchased from Sino Biological (Beijing, China): SARS-CoV-2 recombinant Spike RBD wild type, RBD (S477N), RBD (Y453F), RBD (K458R), RBD (F342L), RBD (V367F), RBD (N354D), RBD (A435S), RBD (V483A), RBD (W436R), RBD


  The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia.
 PMID: 34533304       2021       ACS chemical neuroscience
Discussion: For example, the virus with the N501Y mutation has similar binding to ACE2, while the K417N and the E484K mutants may have slightly increased binding to ACE2.


  In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2.
 PMID: 34534263       2021       PLoS pathogens
Method: The receptor binding domain of Spike is from amino acids 319-541: B1.351 and P1 had 3 mutations in the RBD (K417N/T, E484K and N501Y) while Alpha (B.1.1.7) only had one (N501Y).
Method: We used the following amino acids replacements and deletions in
Result: It is important to stress these emerging variants of concern, collectively, share a combination of three amino acid mutations in spike receptor binding domain (RBD): N501Y common to all and K417N and E484K in the Brazil and South African variants.


  Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity.
 PMID: 34536797       2021       Virology
Introduction: Similarly, the E484K and K417N/T mutations in the RBD that were first described in the B.1.351 and P.1 lineages likely due to immune evasion from vaccine or natural infection-elicited antibodies, are now present in several other lineages.
Result: Although both K417N and K417T presented a modest increase in the on-rate kinetic by ~1.56 and ~1.11 folds, the accelerated off-rate kinetics dictated the overall decrease affinity of these mutants.
Result: Interestingly, three mutations/deletion in this VOC decreased the interaction with ACE2-Fc, namely R246I and Delta242-244 in the NTD, as well as K417N in the RBD.


  The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages.
 PMID: 34537136       2021       Cell
Result: In addition to the 29 convergent mutations that displayed frequency increases between March 15 and June 1, 2021, the meta-signature includes deletion mutations at ORF1a/3675-3677, S/69-70, S/144, and S/241-243 (which, while displaying convergence between the different 501Y lineages, were not amenable to selection analyses) and the convergent signature substitutions L18F, K417N/K, and N501Y (which were already at high frequencies in multiple 501Y lineages by March 15, 2021).
Result: In this regard, while mutations at S/20, S/80, S/138, S/215, and S/570 in different lineages do not predominantly converge on the same encoded amino acid states, they could nevertheless still be convergent on similar fitness objectives (immune escape or compensation for the fitness costs of other mutations): such as is likely the case with the also not strictly


  Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants.
 PMID: 34543625       2021       The Journal of biological chemistry
Abstract: Compared with the wildtype, four mutants (K417N, Y453F,
Introduction: These include 9 single site mutations K417N, N439K, Y453F, S477N, S477I, T478I, E484K, S494P and N501Y (Alpha variant), a double mutant (E484K/N501Y) and two triple mutants (K417N/E484K/N501Y (Beta variant) and K417T/E484K/N501Y (Gamma variant)).


  Review of the mechanisms of SARS-CoV-2 evolution and transmission.
 PMID: 34545334       2021       ArXiv
Abstract: We predict that RBD co-mutation [A411S<
Conclusion: We forecast that a few co-mutation sets, including [A411S, L452R, T478K], [L452R, T478K, N501Y], [K417N, L452R, T478K], [L452R, T478K, E484K, N501Y], and [P384L, K417N, E484K, N501Y], have a great potential to grow into unprecedentedly dangerous new SARS-CoV-2 variants.


  The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2.
 PMID: 34547629       2021       Biochemical and biophysical research communications
Introduction: In particular, three mutations (K417T, E484K, and N501Y) in RBD (Receptor Binding Domain) are common in Alpha (N501Y) and Beta (K417 N, E484K, and N501Y) which are associated with increased transmissibility, immune escape and pathogenicity.



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