Result: Individual mutations N501Y, K417N and E484K, and N439K mutation (widespread in Europe), had only a marginal impact on the antibody binding.
Figure: (a, b) Binding of the antibodies to the RBD carrying the individual mutations (N501Y, N439K, E484K, K417N) and RBD with triple mutation N501Y/E484K/K417N were analysed.
Figure: ACE2 is shown in a green cartoon model, RBD as a grey surface model, mutations N439K (within AX677 binding site) and
Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach.
Result: Considering several parameters, including estimated informedness and amplicon lengths, we observed that the subset comprising the SNPs K417N, N439K, Y453F, S477N, T478K, E484K, N501Y, A570D, H655Y, Q677H, P681H, I692V, A701V, and716I, would lead to a test providing an acceptable compromise between informedness (0.76) and minimal amplicon length (896 bp).
Table: N439K
Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift.
Figure: As an example of nomenclature, Alpha+2muts (N439K) represents the first two mutations with the highest mutation frequency introduced on the Alpha variant and the last site added is N439K.
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
Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context.
Abstract: By using our pipeline, we built 3D comparative models of the SARS-CoV-2 spike RBD/ACE2 protein complexes for the VoC B.1.1.7-United Kingdom (carrying the mutations of concern/interest N501Y, S494P, E484K at the RBD), P.1-Japan/Brazil (RBD mutations: K417T, E484K, N501Y), B.1.351-South Africa (RBD mutations: K417N, E484K, N501Y), B.1.427/B.1.429-California (RBD mutations: L452R), the B.1.141 (
Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor.
PMID: 34955621
2022
Journal of King Saud University. Science
Introduction: Substitution mutations like D614G, N501Y, Y453F, N439K/R, P681H, K417N/T, and E484K, as well as deletion mutations like DeltaH69/V70 and Delta242-244 are the most common in the spike protein.
Analysis of SARS-COV2 spike protein variants among Iraqi isolates.
Introduction: Another variant possesses N439K mutation in the receptor-binding domain (RBD) of spike protein has also been reported independently in many countries in Europe and the USA.
Introduction: The N439K variant has shown to have increased pathogenicity and can escape from neutralizing monoclonal antibodies and reducing the activities of some polyclonal responses.
Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations.
PMID: 34801754
2022
Infection, genetics and evolution
Result: S477N was observed in 18,219 sequences, and N439K was observed in 6743 sequences.
Result: The RBD substitution N439K has slowly increased in prevalence since August 2020 and has been consistently observed in 2.0-4.5% of samples worldwide since the week of August 16th.
Discussion: The RBD variant N439K, which has been shown to result in antibody evasion, is becoming more common over time.
SARS_CoV_2 mutation literature information.
PMID: 
2022
International immunopharmacology
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