literature

SARS_CoV_2 mutation literature information.

mRNA-1273 Vaccine-elicited Neutralization of SARS-CoV-2 Omicron in Adolescents and Children.

PMID: 35118475 2022 medRxiv

Method: The Omicron (B.1.1.529) variant contained spike mutations A67V, Delta69-70, T95I, G142D, Delta143-145, Delta211, L212I, +214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K,

Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach.

PMID: 35062327 2022 Viruses

Introduction: Last in order of arrival but certainly not least, the variant called Omicron (B.1.1.529) is characterized

Result: Considering several parameters, including estimated informedness and amplicon lengths, we observed that the subset comprising the SNPs K417N, N439K, Y453F, S477N, T478K, E484K, N501Y, A570D, H655Y, Q677H, P681H, I692V, A701V, and716I, would lead to a test providing an acceptable compromise between informedness (0.76) and minimal amplicon length (896 bp).

Table: H655Y

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

PMID: 35078012 2022 EBioMedicine

Method: It is the ectodomain of SARS-CoV-2 spike protein expressed in HEK293 cells, which contains amino acids Val16 - Pro1213 of Spike (GenBank: QHD43416.1) with T4 fibritin trimerization motif, a polyhistidine tag at the C-terminus, proline substitutions (F817P, A892P, A899P, A942P, K986P, V987P) and alanine substitutions (R683A and R685A) to stabilize the trimeric pre-fusion conformation, and mutations identified in the Omicron variant (A67V, HV69-70del, T95I, G142D, VYY143-145del, N211del,

Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants.

PMID: 35090164 2022 Nature

Method: In additional to the reported mutations (A67V, Delta69-70, T95I, G142D, Delta143-145, Delta211, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G,

PMID: 35101265 2022 Vaccine

Table: H655Y

Divergent SARS-CoV-2 Omicron-reactive T and B cell responses in COVID-19 vaccine recipients.

PMID: 35113647 2022 Science immunology

Method: The omicron variant contained the following spike mutations: A67VS, del69-70, T95I, G142-, del143-144, Y145D, del211, L212I, ins215EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G,

Breadth of SARS-CoV-2 Neutralization and Protection Induced by a Nanoparticle Vaccine.

PMID: 35118474 2022 bioRxiv

Method: D614G spike mutation: D614G; Alpha (B.1.1.7) spike mutations: Delta69-70, Delta144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H; Beta (B.1.351) spike mutations: L18F, D80A, D215G, Delta242-244, R246I, K417N, E484K, N501Y, D614G, A701V; Delta (B.1.61

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.

SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity.

PMID: 35233544 2022 Cell reports. Medicine

Method: The SARS-CoV-2 Wuhan-1 spike, cloned into pCDNA3.1 was mutated using the QuikChange Lightning Site-Directed Mutagenesis kit (Agilent Technologies) and NEBuilder HiFi DNA Assembly Master Mix (NEB) to include D614G (original) or lineage defining mutations for Alpha (DEL69-70, DEL144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H), Beta (L18F, D80A, D215G, 242-244del, K417N, E484K, N501Y,

Table: H655Y

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: In addition, fifteen other substitutions affect the spike protein including Q954H, N764K, H655Y, K417N, G339D, N211K, Q493R, S371L, S373P, S375F, S477N, T478K, E484A, N440K and G446S were detected as the most frequent mutation events in more than 84% of total genomes.

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