literature

SARS_CoV_2 mutation literature information.

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,

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

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.

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

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,

Occurrence of a novel cleavage site for cathepsin G adjacent to the polybasic sequence within the proteolytically sensitive activation loop of the SARS-CoV-2 Omicron variant: The amino acid substitution N679K and P681H of the spike protein.

PMID: 35436320 2022 PloS one

Result: In a first set of investigations, a prediction approach of cleavage sites for the SARS-CoV-1 660YHTVSLLRSTSQKS673, SARS-CoV-2 (Wuhan) 678TNSPRRARSVASQS691, SARS-CoV-2 P681H (Alpha) 678TNSHRRARSVASQS691, and SARS-CoV-2 P681R (Delta) 678TNSRRRARSVASQS691, SARS-CoV-2 N679K (C.1.2) 674YQTQTKSPRRARSVASQS691, and SARS-CoV-2 N679K P681R (Omicron) 674YQTQTKSHRRARSVASQS691.

Result: In order to verify these results experimentally, SARS-CoV-1, SARS-CoV-2 (Wuhan), SARS-CoV-2 P681H (Alpha), and SARS-CoV-2 P681R (Delta), SARS-CoV-2 N679K (C.1.2), and SARS-CoV-2 N679K P681R (Omicron) peptides were synthesized and incubated with the indicat

Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy).

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: 35336868 2022 Viruses

Introduction: Omicron has posed a serious public health concern due to the mutations/deletions associated with increased binding affinity to ACE2 (S:Q498R and S:N501Y), increased transmissibility (S:H655Y, S:N679K, and S:P681H), increased viral load (N:R203K and N:G204R), innate immune evasion (ORF1a:L3674-, ORF1a:S3675-, and ORF1a:G3676), and S-gene target failure (S:H69-).

Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein.

PMID: 35333910 2022 PloS one

Abstract: None of the mutations increased but several decreased S protein cleavage at the S1/S2 site, including S686G and P681H, the latter of which is found in variants of concern B.1.1.7 (Alpha variant) and B.1.1.529 (Omicron variant).

Discussion: A total of five mutations (P681H, P681L, A684S, S686G, V687L) were found to be associated with reduced S protein cleavage, with mutation S686G showing the lowest level of S protein cleavage.

Discussion: In contrast, Lubinski and colleagues and the present study demonstrate that P681H, which is found in the

Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants.

PMID: 35337015 2022 Viruses

4Method: By using this approach, we generated two Omicron ""specific"" targets (A67V

7Figure: Omicron variant (Non-BA.2) sequences are expected to contain A67V + del-HV69-70 (probe 1, ""SDEL2""), E484A (probe 3, ""E484A"") and N679K + P681H (probe 4, ""P681H"")."

Abstract: Analytic sensitivity was determined as 19.0 IU/mL (CI95%: 12.9-132.2 IU/mL) for the A67V + del-HV69-70 target, 193.9 IU/mL (CI95%: 144.7-334.7 IU/mL) for the E484A target, 35.5 IU/mL (CI95%: 23.3-158.0 IU/mL) for the N679K + P681H target and 105.0 IU/mL (CI95%: 80.7-129.3 IU/mL) for the P681R target.

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