Abstract: To build an investigative framework, we have applied an unsupervised machine learning approach to 4296 Omicron viral genomes collected and deposited to GISAID as of December 14, 2021, and have identified a core haplotype of 28 polymutants (A67V, T95I, G339D, R346K, Introduction: Most of these mutations (G339D, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H) present on the RBD surface.
Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy).
Result: Finally, 1/32 sequence was the Omicron strain, with the following mutations in the RBD domain: T22882G (N440K), G22898A (G446S), G22992A (S477N), C22995A (T478K), A23013C (E484A), A23040G (Q493R), G23048A (G496S), A23055G (Q498R), A23063T (N501Y), T23075C ( PMID: 35271889
2022
Journal of virological methods
Introduction: B.1.617 variant with three sublines, including B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.617.3 which are recognized according to three amino acid mutations, L452R, T478K, and E484Q.
Introduction: Delta as a variant of concern (VOC) possesses L452R and T478K mutation, while the two other subtypes of B.1.617 cited with L452R and E484Q mutation.
Figure: Schematic of the mutations del69-70, E484K, E484Q, D614G, L452R, and T478K that were selected for dominant variant screening.b.
Figure: The presence of A) L452R
Proteolytic activation of SARS-CoV-2 spike protein.
Introduction: Instead, it has L452R and T478K mutations.
Introduction: Similar to the alpha variant, the S protein of the delta variant has the P681R mutation in addition to L452R and T478K (Figure 5).
Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics.
PMID: 35285246
2022
Applied and environmental microbiology
Abstract: Using next-generation sequencing (NGS) of the spike (S) gene amplicons of the Delta variant-dominant samples, we found six mutations exclusive to the Delta variant (S:T19R, S:Delta156/157, S:L452R, S:T478K, S:P681R, and S:D950N).
Result: Importantly, this mutation has higher sensitivity and specificity in both regions of interest than the mutation S:T478K (sensitivity is 0.99 and specificity is 0.97 in Illinois, while sensitivity is only 0.96 and specificity is only
Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections.
Introduction: B.1.617.2, which was confirmed in India, has mutations (L452R and T478K) in the RBD, leading to higher viral load in infected individuals, in addition to the P681R mutation which increases the virus transmissibility.
Introduction: Finally, B.1.1.529, which was detected in Botswana on November 11, 2021 and South Africa on November 14, 2021, has 15 mutations (G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R,
Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations.
Abstract: N501Y, E484K, K417N, K417T, L452R and T478K in the receptor binding domain (RBD) region may increase the infectivity in several variants of SARS-CoV-2.
Abstract: In this study, we discovered that GB-1, developed from Chiehyuan herbal formula which obtained from Tian Shang Sheng Mu of Chiayi Puzi Peitian Temple, can inhibit the binding between ACE2 and RBD with Wuhan type, K417N-E484K-N501Y and L452R-T478K mutation.
Abstract: Our results suggest that GB-1 could be a potential cand
SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines.
Introduction: According to US FDA reports, the mAb cocktail retained neutralization activity against B.1.1.7 (carrying N501Y) and B.1.617.2/AY.3 (carrying L452R + T478K).
Introduction: And cilgavimab had lower activity against N501Y+D614G mutants, including B.1.429 (carrying L452R), B.1.617.2 (carrying L452R + T478K) and B.1.351 (carrying K417N + E484K + N501Y).
Introduction: Specific mutations in the RBD of omicron, namely T478K, Q493K, Q498R, and
Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination.
Result: including N501Y in both Alpha and Beta, E484K in Eta and Beta, K417N in Beta, and L452R and T478K only in Delta.
Discussion: Amino acid changes in spike proteins of variants contribute to immune evasion, and it has been suggested that N501Y is associated with increased infectivity, whereas L452R, T478K, and E484K with K417N reduce the interaction of neutralizing antibodies with RBD.
Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant.
8Discussion: Hence, some bioinformatic models predicted an increase in the ACE2 binding affinity of Omicron RBD while other models rejected this scenario and stated: ""the Q493R/K mutations, in a combination with K417N and T478K, dramatically reduced the S1 RBD binding by over 100 folds""."
Discussion: S477N, T478K, and E484A were initially at ~47% (status 2021-12-14, 2146 sequences), now instead above 88%, as N501Y (status 2022-02-07, 873.492 sequences).
Discussion: Several Omicron RBD mutations are assumed to increase the binding to ACE2: G339D, S477N,
SARS_CoV_2 mutation literature information.
PMID: 
2022
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