literature

Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern.

PMID: 35078012 2022 EBioMedicine

Result: We have performed a test of binding of chimeric antibodies AX677ch and AX290ch to the ectodomain trimer of the Omicron S protein (carrying mutations A67V, HV69-70del, T95I, G142D, VYY143-145del, N211del, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R,

PMID: 35062327 2022 Viruses

Introduction: Last in order of arrival but certainly not least, the variant called Omicron (B.1.1.529) is characterized by more than thirty mutations on the spike gene only, many of these unique (E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, H655Y, and N679K) while others are shared with other lineages (for example T478K with Delta and P681H with Alpha and Mu).

Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies.

PMID: 35016194 2022 Nature

Method: Omicron pseudovirus contains the following mutations: A67V, H69del, V70del, T95I, G142D, V143del, Y144del, Y145del, N211del, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R,

PMID: 34754982 2022 Gene reports

Abstract: Twenty-two distinct mutations were identified within the spike protein regions which were: L5F, L18F, T19R, S151T, G181A, A222V, A348S, L452 (Q or M), T478K, N501Y, A520S, A522V, A570D, S605A, D614G, Q675H, N679K, P681H, T716I, S982A, A1020S,

PMID: 34906769 2022 Biomedicine & pharmacotherapy

Table: N679K

The significant immune escape of pseudotyped SARS-CoV-2 variant Omicron.

PMID: 34890524 2022 Emerging microbes & infections

Result: There are 32 mutations on the Spike of Omicron, including the following sites: A67V, H69del-V70del, T95I, G142D-V143del-Y144del-Y145del, N211del-L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H,

PMID: 34801754 2022 Infection, genetics and evolution

Result: S17) reveals 14 mutations out of 64 total that appear to be consistently present (P681H, Q677H, Q675H, Q677P, S673T, N679K, P681R, Q675R, P681L, T676I, T678I, A684V, Q677R, and A672V).

Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach.

PMID: 34307771 2021 Virusdisease

Table: N679K

Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner.

PMID: 34452511 2021 Viruses

Result: The 03-23 S1S2 sample had a sequence '1841G(D614G) 2037G(N679K) 2063T(A688V)'.

Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations.

PMID: 34458642 2021 Heliyon

Figure: Mutated amino acid positions shown in the human ACE2 receptor bound structure (PDB ID: 6acj) of SARS-CoV-2 spike protein (except L5F, S13I, Q14H, G75V, T76I, Y145del, H146Y, Q675 H/R, Q677H, N679K, I834V, R1185H and K1195N as the regions were not covered in the structure).