literature

SARS_CoV_2 mutation literature information.

Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes.

PMID: 35062348 2022 Viruses

Introduction: The Spike of Mu accumulated the following mutations: insertion in 146N, T95I, Y144T and Y145S, in the N-terminal domain (NTD); R346K, E484K, N501Y in the receptor-binding domain (RBD) and P681H at the S1/S2 interface.

Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India.

PMID: 35065253 2022 Microbial pathogenesis

Discussion:

Discussion: Alpha variant B.1.1.7 was found in one case each from vaccine breakthrough, mild and dead patient category showing nonsynonymous mutations of N501Y, A570D, D614G, P681H, T716I, S982A, D1118H and three deletions of H69del, V70del, and Y144del.

Discussion: Further, P681H in Alpha disrupts the furin cleavage site by changing the Proline to improve the rate of membrane fusion, virus entry, and higher transmissibility, albeit less efficiently than Delta variant manifesting P681R.

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,

Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability.

PMID: 35163572 2022 International journal of molecular sciences

Introduction: S-B.1.1.7 variant of the SARS-CoV-2 has 9 of the 17 mutations (Delta69-70 deletion, Delta144 deletion, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H) in the S protein, featuring N501Y mutation, which can increase binding affinity with ACE2 while eliciting immune escape from RBD-targeting antibodies.

Method: A systematic mutational scanning and sensitivity analysis of the functional RBD residues (K417, E484, N501), S-B.1.1.7 mutational sites (N501Y, A570D, P681H,

Linked nosocomial COVID-19 outbreak in three facilities for people with intellectual and developmental disabilities due to SARS-CoV-2 variant B.1.1.519 with spike mutation T478K in the Netherlands.

PMID: 35139811 2022 BMC infectious diseases

Introduction: Additionally, B.1.1.519 shares the P681H mutation with the B.1.1.7 variant, which is near the furin-cleavage site and could have an effect on viral entry.

Result: Since the B1.1.519 lineage harbors a few mutations of interest in the spike protein including the T478K mutation (Additional file 1: Figure S1) and the P681H mutation as established in several other lineages, including the B.1.1.7 variant, we studied whether samples harboring this genotype contained higher viral loads compared to isolates belonging to the B.1.1.7 or other variants.

Discussion: Increased infectiousness of the B.1.1.519 variant could explain the high prevalence in Mexico and rapid transmission in our linked outbreak and could be caused by the T478K mutation or P681H which is shared with

SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021.

PMID: 35130727 2022 mBio

Result: The spike substitution P681H was also slightly enriched; this substitution is near the furin cleavage site and may promote efficient proteolysis.

Amplification Artifact in SARS-CoV-2 Omicron Sequences Carrying P681R Mutation, New York, USA.

PMID: 35130474 2022 Emerging infectious diseases

Introduction: A total of 59 samples showed P681H on this repeated testing; only 2 still showed P681R, 1 at 0.52 frequency (down from 0.98) and 1 at 0.94, exactly as the previous sequence, suggesting a true P681R call, possibly co-infection with Delta, because the Ct for this sample was low (Ct = 17).

Introduction: Closer examination indicated that the Omicron sequences with P681R contained varying numbers of P681H reads (median frequency of P681R call, a G at nucleotide position 23604, was 0.79 [range 0.43-0.98]).

Introduction: Of the 379 samples, amplified using 24 cycles regardless of cycle threshold (Ct), we detected 86 with P681R, a key Delta mutation associated with increased transmissibility, fusogenicity, and pathogenicity, distinct

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,

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: 35078012 2022 EBioMedicine

Result: We have performed a test of binding of chimeric antibodies AX677ch and AX290ch to the ectodomain trimer of the Omicron S protein (carrying mutations A67V, HV69-70del, T95I, G142D, VYY143-145del, N211del, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R,

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