literature

SARS_CoV_2 mutation literature information.

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.

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.

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,

Origin of the tight binding mode to ACE2 triggered by multi-point mutations in the omicron variant: a dynamic insight.

PMID: 35373810 2022 Physical chemistry chemical physics

Abstract: Multi-point mutations in the Omicron variant RBD could cause the conformation shift in the large Loop (where T478K and E484A are located), which makes it easier to wrap the N-terminal helix of ACE2 and form tighter contacts.

Abstract: This was due to the large number of positively charged patches (N440K, T478K, Q493R, Q498R, and Y505H) formed by the substitution of neutral amino acids at multiple sites.

Protective Immunity of the Primary SARS-CoV-2 Infection Reduces Disease Severity Post Re-Infection with Delta Variants in Syrian Hamsters.

PMID: 35337002 2022 Viruses

Introduction: AY.1 has amino acid substitutions at T19R, E156G, 157/158 del, W258L, K417N, L452R, T478K, D614G, D950N and P681R.

Introduction: The amino acid substitutions in the spike protein of the Delta variant, such as D614G, T478K, P681R and L452R, are known to affect transmissibility and neutralization.

Method: Delta AY.1 variant had D614G, E156G, F157del,

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: 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, Introduction: Most of these mutations (G339D, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H) present on the RBD surface.

Role of the Microbiome in the Pathogenesis of COVID-19.

PMID: 35433495 2022 Frontiers in cellular and infection microbiology

Table: T478K

The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia.

PMID: 35341058 2022 PeerJ

Abstract: Additionally, the S_T19R, S_E156G, S_F157del, S_R158del, S_L452R, S_T478K, S_D950N and S_V1264L changes were only detected in Delta va

Result: We also observed that Delta variants carried various amino acid changes that differ from the first wave, which included changes within the spike protein, namely S_T19R, S_G142D, S_E156G, S_F157del, S_R158del, S_L452R, S_T478K, and S_D950N.

Insights from computational analysis: how does the SARS-CoV-2 Delta (B.1.617.2) variant hijack ACE2 more effectively?

PMID: 35364605 2022 Physical chemistry chemical physics

Abstract: The results showed that the existence of L452R and T478K mutations can trigger the effective hijacking of ACE2 by the Delta variant through the following three ways: (i) these two mutations can significantly enhance the electrostatic energy of the system by the introduction of two positively charged amino acids (Arg and Lys), thereby increasing the binding affinity of RBD and ACE2, (ii) the Loops 1, 3, and 4 in the receptor-binding motif (RBM) of RBD form a tighter conformation under the dominance of the T478K mutation, allowing ACE2 to be captured more effectively than the wild-type system, and (iii) these conformational changes lead to a more stable hydrogen bond in the Delta variant, which further ensures the stability of the binding.

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