Introduction: Omicron has posed a serious public health concern due to the mutations/deletions associated with increased binding affinity to ACE2 (S:Q498R and S:N501Y), increased transmissibility (S:H655Y, S:N679K, and S:P681H), increased viral load (N:R203K and N:G204R), innate immune evasion (ORF1a:L3674-, ORF1a:S3675-, and ORF1a:G3676), and S-gene target failure (S:H69-).
Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil.
Result: AA deletions covering in the NTD region (Delta144, Delta141-144 and Delta138-143) and substitutions at the S1/S2 junction (N679K, P681H and P681R), however, were particularly prevalent and sharply increase from January to May 2021.
Result: During June-July 2021, the proportion of P.1+N679K genomes continued to increase up to 76.9%, the relative frequency of P.1+P681H genomes increased up to 37.1% in June and then decrease to 13.5% in July, while the frequency of variants P.1+NTDdel dropped to 2.1%.
Result: Inspection of P.1 sequences available at EpiCoV database in the GISAID
Figure: Maximum likelihood phylogenetic tree of P.1 Amazonian sequences and P.1+NTDdel, P.1+N679K, and P.1+P681H sequences detected outside Amazonas.
In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility.
Result: The amino acid substitutions (D614G, D614G, D796Y, T547K, N856K, N679K, N969K, P681H, L981F) in the spike protein, P314L, A1892T, T492I, I189V and A1892T in the non-structural proteins (NSP3, NSP4, NPS6, and NSP12b) occurred in 100% of analyzed SARS-CoV-2 genomes.
Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy.
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, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H,
Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions.
Abstract: We also evaluated mutations in the antibody-binding regions and observed some important mutations overlapping those of previous variants including N501Y, D614G, H655Y, N679K, and P681H.
Introduction: Some mutations including T478K,
Discussion: The significant mutations and features are N501Y (augments the binding between of S-protein and ACE2); D614G (increase infectivity); H655Y (accelerate transmission); N679K (increase viral transmission); and P681H (enhance binding affinity of S-protein) (Table 2).
SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines.
SARS_CoV_2 mutation literature information.
PMID: 
2022
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