literature

SARS_CoV_2 mutation literature information.

Impact of new variants on SARS-CoV-2 infectivity and neutralization: A molecular assessment of the alterations in the spike-host protein interactions.

PMID: 35194576 2022 iScience

Abstract: The substitutions T478K and L452R in the Delta variant enhance associations with ACE2, whereas P681R promotes recognition by proteases, thus facilitating viral entry.

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

PMID: 35207518 2022 Life (Basel, Switzerland)

Introduction: Some concerning S mutations are K417N, T478K, N501Y and D614G, all of which are found in the previous VOCs and responsible in the increased viral transmission and enhanced immune invasion.

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

Abstract: Phylogenetic analysis of SARS-CoV-2 genomes revealed the existence of eleven GISAID clades with GR (variant of the spike

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.

Characterization of a Broadly Neutralizing Monoclonal Antibody against SARS-CoV-2 Variants.

PMID: 35215823 2022 Viruses

Introduction: It has been reported that several mutations in the SARS-CoV-2 RBM, such as N439K, L452R, S477N, T478K, E484K, S494P, N501Y, and A502S, have increased the infectivity and stability of SARS-CoV-2.

Discussion: Early research on the Omicron variant has shown multiple mutations in the RBM such as N440K, G446S, S477N, T478K, Q493K, G496S, Q498R, N501Y, Y505H, including a mutation residin

Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant.

PMID: 35216287 2022 International journal of molecular sciences

Introduction: Strikingly, K417N, T478K, G496S, Y505H, and the triple S371L, S373P, S375F can reduce affinity to ACE2 while driving immune evasion and providing a final net affinity for ACE2 similar to the original virus.

Result: Moreover, it was proposed that K417N, T478K, G496S, Y505H, and the mutations at the cryptic epitope S371L, S373P, S375F can reduce affinity to ACE2 while driving immune evasion.

Result: We also examined the effect of Omicron mutations in the

PMID: 35223905 2022 Frontiers in medicine

Method: For instance, a Delta variant spike haplotype consisting of T19R, 256_258delinsG, L452R, T478K, D614G, P681R, and D950N is also assigned to another haplotype group of T19R, L452R, T478K, D614G, P681R, and D950N, which is missing a 256_258delinsG variant.

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, D614G and A701V<

SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies.

PMID: 35380448 2022 Science translational medicine

Result: We compared the neutralization titers of these serum samples against pseudoviruses bearing spike proteins from the following variants: D614G, Omicron (A67V, del69-70, T95I, del142-144, Y145D, del211, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R,

Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage.

PMID: 35396511 2022 Nature communications

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 (wild-type) or lineage defining mutations for Beta (L18F,

Result: Additional substitutions include P25L (in ~43% of viruses) and W152R (in ~7%) in the NTD, T478K (~17%) in the RBM, L585F (~17%) in S1, P681H (~8%) adjacent to the furin cleavage site, A879T (~7%), D936H (~5%), and H1101Q (~8%) in S2, with additional amino acid changes detected in less than 5% of viruses.

Immune evasion and chronological decrease in titer of neutralizing antibody against SARS-CoV-2 and its variants of concerns in COVID-19 patients.

PMID: 35398519 2022 Clinical immunology (Orlando, Fla.)

Introduction: This lineage has three main subtypes: B.1.617.1 (Kappa variant) and B.1.617.3, characterized by L452R and E484Q mutation in RBD, and B.1.617.2 (Delta variant), characterized by L452R and T478K in RBD.

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