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
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 0.98 in the United State [Fig.
Result: Therefore, our analysis shows that the PCR assay targeting S:T478K would estimate that the Delta variant was dominant from January 2021 to October 2021, when in reality, Delta variant sequences were collected and later deposited in GISAID starting in May 2021.
Result: This lineage accounted for only around 1.2% of sequences from the United States (n = 1,187,412, from January 2021 to October 2021), so the PCR assay targeting S:T478K was expected to work well for Illinois, USA, showing an estimated sensit
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.
Result: L452R and T478K mutations of RBD in delta variant could induce a strong immune escape ability.
Result: After treatment of the cells with GB-1, the number of 293 T cells with high binding to the RBD with L452R-T478K mutation was significantly decreased in both ACE2-positive cells and the top population in GB-1 treatment group .
Result: Effect of GB-1 on the binding between ACE2 and RBD with L452R-T478K mutation.
Result: Next, we investigated the effect of GB-1 on the binding between ACE2 and RBD with L452R-T478K mutation through dual-color flow cytometric analysis.
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""."
Table: T478K
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:
ViMRT
SARS_CoV_2 mutation literature information.
PMID: 
2022
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