Evaluation of a Rapid and Accessible Reverse Transcription-Quantitative PCR Approach for SARS-CoV-2 Variant of Concern Identification.
PMID: 35465708
2022
Journal of clinical microbiology
Abstract: We designed and analytically validated a two-reaction multiplex reverse transcription-quantitative PCR (RT-qPCR) assay targeting spike protein mutations L452R, E484K, and N501Y in reaction 1 and del69-70, K417N, and T478K in reaction 2.
Binding Interactions between Receptor-Binding Domain of Spike Protein and Human Angiotensin Converting Enzyme-2 in Omicron Variant.
PMID: 35481766
2022
The journal of physical chemistry letters
Abstract: Other mutations, such as K417N, G446S, and Y505H, decrease the ACE2 binding, whereas S447N, Q493R, G496S, Q498R, and N501Y tend to increase it.
RBD-mRNA vaccine induces broadly neutralizing antibodies against Omicron and multiple other variants and protects mice from SARS-CoV-2 challenge.
Abstract: The RBD-mRNA-induced antibodies exerted moderate neutralization against authentic B.1.617.2 and B.1.1.529 variants, and pseudotyped B.1.351 and P.1 lineage variants containing K417N/T, E484K, and N501Y mutations, the B.1.617.2 lineage variant harboring L452R, T478K, and P681R mutations, and the B.1.1.529 lineage variant containing 38 mutations in the S protein.
Abstract: The vaccine induced durable antibodies that potently neutralized prototypic strain and B.1.1.7 lineage variant pseudoviruses containing N501Y or D614G mutations alone or in combination with a N439K mutation (B.1.258 lineage)
Convergent Evolution of Multiple Mutations Improves the Viral Fitness of SARS-CoV-2 Variants by Balancing Positive and Negative Selection.
Abstract: N501Y increases receptor binding; however, it has decreased stability and expression.
Abstract: Triple mutant K417T/E484K/N501Y has increased receptor binding, escapes both Class 1 and Class 2 antibodies, and has similar stability and expression as that of the wild-type.
Abstract: We examined the physical mechanisms underlying the convergent evolution of three mutations K417T/E484K/N501Y by delineating the individual and collective effects of mutations on binding to angiotensin converting enzyme 2 receptor, immune escape from neutralizing antibodies, protein stability, and expression.
Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival.
PMID: 33834772
2022
Journal of medicinal chemistry
Figure: MD simulation of the RBD-ACE2 complex with the N501Y, K417N, and E484K mutations in the RBD.
Discussion: In the South Africa variant (501Y.V2), actually there are two more mutations, N501Y and E484K.
Discussion: Therefore, the gain from the improved RBD-ACE2 binding that resulted from both N501Y and E484K mutations might be enough to compensate for the loss caused by the K417N mutation and is likely to yield an interaction with ACE2 even stronger than that of the wild-type virus.
Discussion: To explore their contributions, we carried out MD simulation for the
Abstract: In pseudovirus neutralization studies, LY-CoV1404 retains potent neutralizing activity against numerous variants including B.1.1.7, B.1.351, B.1.617.2, B.1.427/B.1.429, P.1, B.1.526, B.1.1.529, and the BA.2 subvariant and retains binding to spike proteins with a variety of underlying RBD mutations including K417N, L452R, E484K, and N501Y.
Abstract: Notably, the binding and neutralizing activity of LY-CoV1404 is unaffected by the most common mutations at these positions (N439K and N501Y).
Post-Vaccination Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infections and Incidence of the Presumptive B.1.427/B.1.429 Variant Among Healthcare Personnel at a Northern California Academic Medical Center.
Abstract: Available specimens were tested for L452R, N501Y, and E484K mutations using reverse-transcription polymerase chain reaction.
Less Frequent Sequence Mismatches in Variants of Concern (VOCs) of SARS-CoV-2 in the Real-Time RT-PCR Assays Developed by the National Institute of Infectious Diseases, Japan.
PMID: 34193667
2022
Japanese journal of infectious diseases
Abstract: The frequency of mismatched sequences in three variants (GRY/VOC202012/01, GH/N501Y.V2, and GR/N501Y.V3) was lower than that in all SARS-CoV-2 sequences.
Abstract: The variants GRY/VOC202012/01 (B1.1.7), GH/N501Y.V2 (B1.351), and GR/N501Y.V3 (P1) are characterized by N to Y amino acid substitution at position 501 in the S protein.
Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction.
Abstract: Interestingly, combining mutations E484K, K417N, and N501Y resulted in a RBD with both features: enhanced receptor binding and abolished immune reco
Discussion: A previous study has shown that serum neutralization is not compromised by N501Y (also found in the strain B.1.1.7).
Discussion: The variant with the mutation N501Y shows enhanced affinity but almost normal recognition by convalescent antibodies.
Discussion: When we investigated whether distinct mutations may affect receptor affinity, we found that N501Y mutation enhanced affinity for the viral receptor ACE2 both as a single mutation and as a triple mutation, while E484K mutation alone did not affect the interaction with ACE2.
An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern.
Introduction: Along with multiple mutations in the spike protein, there are 3 specific changes of particular concern: the S: N501Y, shown to enhance the binding affinity to angiotensin-converting enzyme 2 (ACE2), the S: 69-70del that could potentially cause imm
Result: Filtering for more common substitutions (Supplementary Figure 1B) showed a major increase in February in changes associated with B.1.1.7 (eg, S:N501Y, S:A570D, S:T716I, S:S982A, and S:D1118H) while substitutions associated with B.1.2 declined.
SARS_CoV_2 mutation literature information.
PMID: 
2022
Journal of clinical microbiology
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