literature

SARS_CoV_2 mutation literature information.

Host Response to SARS-CoV2 and Emerging Variants in Pre-Existing Liver and Gastrointestinal Diseases.

PMID: 34760721 2021 Frontiers in cellular and infection microbiology

Introduction: This variant of B.1.1.7 lineage harbors receptor-binding domain (RBD) N501Y mutation and other mutations including 69/70 deletion, spike P681H, and ORF8 stop codon (Q27stop) mutation.The beta variant (20H/501Y.V2) of B.1.351 lineage harbors spike N501Y, E484K, and K417N/T mutations without 69/70 deletion and is predicted to have emerged in South Africa during October 2020 with potential of global spread.

CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern.

PMID: 34787487 2021 Microbiology spectrum

Abstract: Our results indicated that the CRISPR-Cas12a assay could readily detect the signature spike protein mutations (K417N/T, L452R/Q, T478K, E484K/Q, N501Y, and D614G) to distinguish alpha, beta, gamma, delta, kappa, lambda, and epsilon variants of SARS-CoV-2.

Introduction: It has been reported that variants with the deletion of amino acids Delta69 and 70 and K417N and E484K mutations in the SARS-CoV-2 S protein are linked to immune response evasion.

Method: The SARS-CoV-2 target sequences include (i) the wild-type (WT) gene fragment of S protein (S

A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology.

PMID: 34787499 2021 Microbiology spectrum

Figure: (a) MS peaks of 9 MPE probes without extension; (b) target site peaks of the MPE probes extended to non-SARS-CoV-2 variants; (c) target site peaks of the MPE probes extended to SARS-CoV-2 S gene mutation plasmid 1 (containing the HV69-70del, K417N, E484K, N501Y, D614G, and P681H mutations); (d) target site peaks of the MPE probes extended to SARS-CoV-2 S gene mutation plasmid 2 (containing the L452R, E484Q, and P681R mutations).

Discussion: In this study, we developed a mPCR-MS minisequencing method that can simultaneously detect 9 mutation types in 7 mutated sites in the RBD of

PMID: 34790980 2021 bioRxiv

Abstract: Against AY.1 pseudoviruses, the L452R and K417N substitutions accounted for the loss of neutralization by four antibodies and one antibody, respectively, whereas one antibody lost potency that could not be fully accounted for by a single RBD substitution.

Abstract: The spike proteins of B.1.617.1, B.1.617.2, and AY.1 variants have several substitutions in the receptor binding domain (RBD), including L452R+E484Q, L452R+T478K, and K417N+L452R+T478K, respectively, that could potentially reduce effectiveness of therapeutic antib

SARS-CoV-2 exposure in Malawian blood donors: an analysis of seroprevalence and variant dynamics between January 2020 and July 2021.

PMID: 34794434 2021 BMC medicine

Method: SARS-CoV-2-pseudotyped lentiviruses were prepared by co-transfecting the HEK 293T cell line with either the SARS-CoV-2 original spike (D614G) or the SARS-CoV-2 beta spike (L18F, D80A, D215G, K417N, E484K, N501Y, D614G, A701V, 242-244 del) plasmids in conjunction with a firefly luciferase encoding pNL4 lentivirus backbone plasmid.

SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene.

PMID: 34796036 2021 Immune network

Introduction: Two mutation sites, E484K and N501Y in critical RBD are identical to that of SARS-CoV-2 alpha variant, whereas K417N does not present in SARS-CoV-2 alpha variant.

Table: K417N

Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants.

PMID: 34805715 2021 ACS omega

Figure: (A) Snapshotsof the effects of the RBD mutations, N501Y, T478K, and K417N; interfaceinteractions and their distribution between ACE2 (red) and the RBD(blue) differed among the mutated states with different RBD movements,determining different dissociation constants Kd.

Figure: (B) Zoomed-in snapshots ofthe H-bond and salt bridge interactions with the K417N<

Figure: (a) Fractional shift (X) variation in the compensatory mutation segments C1, C2, and C3induced by the RBD mutations, E484K, K417N, L452Q, L452R, N501Y, andT478K.

A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features.

PMID: 34806033 2021 Current research in structural biology

Introduction: A sub-lineage of Delta with an additional mutation, K417N is termed as AY.1 (Delta-plus).

Introduction: Another variant from South Africa (B.1.351) emerged independently with multiple mutations in the RBD (K417N and E484K) along with N501Y, however, lacked the 69/70 deletion mutations in the NTD segment.

Result: Further, for the characteristic RBD mutations across VoCs (K417 T/N, L452R, S477N, T478K, E484K, and N501Y), we observed MTR scores between 0.68 and 0.91, suggesting these substitutions to be tolerant.

Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data.

PMID: 34806876 2021 Journal of chemical information and modeling

Abstract: However, Lys417Asn seems to have a compensatory mechanism of action increasing the S1 RBD-ACE2 free energy of binding.

Abstract: The N501Y and K417N mutations in the spike protein of SARS-CoV-2 and their combination gave rise to questions, but the data on their mechanism of action at the molecular level were limited.

Abstract: The K417N mutation in a combination with N501Y fully abolished the antibody effect.

Analysis of BNT162b2- and CVnCoV-elicited sera and of convalescent sera toward SARS-CoV-2 viruses.

PMID: 34820854 2021 Allergy

Abstract: The significance of common VOC mutations K417N, E484K, or N501Y focused on linear epitopes was analyzed using a peptide array approach.

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