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.
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?
Abstract: Phylogenetic analysis of SARS-CoV-2 genomes revealed the existence of eleven GISAID clades with GR (variant of the spike protein S-D614G and nucleocapsid protein N-G204R), GH (variant of the ORF3a coding protein ORF3a-Q57H) and GK (variant S-T478K) being the most common with 25.9%, 19.9%, and 19.6%, respectively, followed by their parent clade G (variant S-D614G) (10.3%).
Result: In addition, fifteen other substitutions affect the spike protein including Q954H
Characterization of a Broadly Neutralizing Monoclonal Antibody against SARS-CoV-2 Variants.
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
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 RBD (G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R
Molecular and Epidemiological Characterization of Emerging Immune-Escape Variants of SARS-CoV-2.
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.
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.
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.
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.
SARS_CoV_2 mutation literature information.
PMID: 
2022
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