literature

SARS_CoV_2 mutation literature information.

Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants.

PMID: 35337015 2022 Viruses

4Method: By using this approach, we generated two Omicron ""specific"" targets (A67V + DEL69/70; and P681H + N679K)."

4Method: For the furin-cleavage-site, probe-4 (""P681H"") also covers N679K with an LNA-base."

7Fig

In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility.

PMID: 35207518 2022 Life (Basel, Switzerland)

Introduction: Moreover, H655Y and N679K mutations are located near the furin cleavage site and may increase S cleavage.

Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect?

PMID: 35208920 2022 Microorganisms

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.

PMID: 35233566 2022 Research square

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.

PMID: 35258772 2022 GeroScience

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.

PMID: 35273977 2022 Frontiers in medicine

Table: N679K

SARS-CoV-2 Omicron variant: Immune escape and vaccine development.

PMID: 35317190 2022 MedComm

Introduction: Specifically, BA.1 and BA.2 display 20 identical spike mutations, which are G339D, S373P, S375F, K417N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K.

Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy).

PMID: 35336187 2022 Microorganisms

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: 35336868 2022 Viruses

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-).

Occurrence of a novel cleavage site for cathepsin G adjacent to the polybasic sequence within the proteolytically sensitive activation loop of the SARS-CoV-2 Omicron variant: The amino acid substitution N679K and P681H of the spike protein.

PMID: 35436320 2022 PloS one

Result: In a first set of investigations, a prediction approach of cleavage sites for the SARS-CoV-1 660YHTVSLLRSTSQKS673, SARS-CoV-2 (Wuhan) 678TNSPRRARSVASQS691, SARS-CoV-2 P681H (Alpha) 678TNSHRRARSVASQS691, and SARS-CoV-2 P681R (Delta) 678TNSRRRARSVASQS691, SARS-CoV-2 N679K (C.1.2) 674YQTQTKSPRRARSVASQS691, and SARS-CoV-2 N679K P681R (Omicron) 674YQTQTKSHRRARSVASQS691.

Result: In order to verify these results experimentally, SARS-CoV-1, SARS-CoV-2 (Wuhan), SARS-CoV-2 P681H

Discussion: Whether the novel cleavage site performed by CatG for SARS-CoV-2 Omicron peptide, carrying the mutations N679K and P681H, might increase infectivity and transmissibility need to be investigated by a cell-based assay.

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