Result: 1B), we did not find the N501Y mutation, which is a characteristic of the UK variant (and shared by the Brazil and SA variants), or the K417N mutation that is found in the Brazil/SA variants.
Result: One sequence each exhibited the N501Y mutation characteristic of the UK strain, an N440K mutation, and no mutation.
Result: Until December 2020, none of the samples exhibited the characteristic mutations (K417N/T, E484K, N501Y, T478K) found in the variants of concern that have been identified so far.
Table: N501Y
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.
Introduction: Africa, mutations of concern/interest: K417N, E484K, N501Y), B.1.427/B.1.429-California (mutations of concern/interest: L452R), the B.1.141 variant (mutations of concern/interest: N439K), the recent B.1.617.1-India (mutations of concern/interest: L452R; E484Q), and the B.1.620 (mutations of concern/interest: namely S477N; E484K).
Introduction: Thus, aiming to test our pipeline and to investigate the effect of amino acid replacement at the SARS-CoV-2 spike RBD, as observed within the most studied VoC, we built a 3D comparative model for each spike variant
Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies.
Method: Hyeryun Choe, The Scripps Research Institute, Jupiter, FL), or S protein with N501Y, E484K, N501Y+E484K or N501Y+E484K+K417N mutations.
Result: In addition to D614G, several other SARS-CoV-2 pseudovirus variants were also tested including D614, N501Y, E484K, N501Y + E484K (N+E), N501Y + E484K + K417N (NEK), R685A.
SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection.
Introduction: Interestingly, despite a much lower mutation rate, recent studies showed that SARS-CoV-2 has the potential to escape neutralizing antibodies, namely by introducing the E484K, N501Y or K417N/E484K spike mutations.
A short plus long-amplicon based sequencing approach improves genomic coverage and variant detection in the SARS-CoV-2 genome.
Abstract: Analysis showed 26 SARS-CoV-2 lineage defining mutations including 4 known variants of concern K417N, E484K, N501Y, P618H in spike gene.
Result: K417N, E484K, N501Y, P618H and variants of interest i.e.
Result: Long-amplicon data captured 20 key lineage defining mutations including spike gene variants of concern K417N, E484K, N501Y and P618H (S3 File).
SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021.
PMID: 35026305
2022
Journal of virological methods
Abstract: We evaluated Allplex SARS-CoV-2 Master Assay and Variants I Assay to detect HV69/70 deletion, Y144 deletion, E484K, N501Y, and P681H spike mutations in 248 positive samples collected in Kuala Lumpur, Malaysia, between January and May 2021.
Introduction: E484K and N501Y mutations are found in B.1.1.7, B.1.351 and P.1.
Method: Samples identified with S mutations and 38 non-variant samples (selected randomly) were then subjected to Allplex SARS-CoV-2 Variants I Ass
Discussion: As omicron carries the spike mutations HV69/70 deletion, Y144 deletion, N501Y, and P681H, both Master and Variants I assays should detect it.
Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift.
Result: Among them, neutralizing activity of aggregated single-point and multipoint mutations on the possible VOCs suggested that the neutralization differences between immunogenic guinea pig sera with diverse mutations were insignificant, of which the immunoprotective effect of D614G + E484K + N501Y immunogen was slightly better than the other three groups.
Result: As indicated in Figure 4D, N501Y in the Gamma RBD induces little conformational change.
Result: For the possible aggregation of multiple mutated VOCs, the changes in their mean NT50 ratios relative to their respective parental VOCs were Ad5-Spike (1.15), mRNA-Spike (0.86), 2019-nCoV (1.28), D614G (1.04), D614G
Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals.
PMID: 35035981
2022
New microbes and new infections
Introduction: In the first patient, we found substitution at position N:S255A and S:N501Y on the first swab and revert back to its original sequence on the second swab and additional substitution at N:R203K and N:S235F.
Introduction: Second patient, we found substitution at position N:R203K and N:S235F on the first swab, additional substitution at ORF1a:T1001I and S:N501Y on the second swab.
Table: PMID: 35056548
2022
Microorganisms
Introduction: This extensive molecular surveillance of the virus has enabled researchers to identify critical mutations that might contribute to higher transmissibility or immune escape, such as D614G, N501Y, and E484K amino acid substitutions in the spike (S) protein.
Discussion: Although the most important substitution in the lineage is considered to be N501Y in the S protein, P681H is adjacent to the furin cleavage site (A684/R685) and may affect the efficiency of cleavage, which facilitates efficient SARS-CoV-2 transmission and infection.
SARS_CoV_2 mutation literature information.
PMID: 
2022
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