E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces.
Introduction: We utilized the L452R, P681R, and E484Q key mutations of Delta, to model the variant's interface against both complexes.
Discussion: Utilizing this real-time tracking of protein interfaces, we have perceived key alterations that cause Delta's clinical characteristics regarding the L452R, P681R, and E484Q spike mutations.
Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions.
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: 35271889
2022
Journal of virological methods
Table: P681R
Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda.
Result: Most of these studies focus on the clinical or experimental observations to demonstrate the danger of mutations, especially the P681R near the furin cleavage site in the SD2-FP domain of the S-protein, but, to the best of our knowledge, no theoretical explanation or computational studies have been reported so far.
Result: Table S2 lists the structure information from VASP optimization for the four SD2-FP models in the Delta variant: (a) wild type (WT), (b) mutated P681R (R681), (c) mutated D614G (G614), and (d) double mutation (DM) labeled as G614-R681.
Discussion: Importantly, the P681R mutation reduces the local rigidity, as evidenced by the NN AABP values (Table 1).
Discussion: The data in Table 1 reveal that D614G and P681R
Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics.
PMID: 35285246
2022
Applied and environmental microbiology
Abstract: Using next-generation sequencing (NGS) of the spike (S) gene amplicons of the Delta variant-dominant samples, we found six mutations exclusive to the Delta variant (S:T19R, S:Delta156/157, S:L452R, S:T478K, S:P681R, and S:D950N).
Result: For the Delta variant, we found three mutations,
Figure: (e and f) Estimated assignment of GISAID samples from Illinois (e) and the United States (f) to variants using the primer designed to target mutation S:P681R.
Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections.
Introduction: B.1.617.2, which was confirmed in India, has mutations (L452R and T478K) in the RBD, leading to higher viral load in infected individuals, in addition to the P681R mutation which increases the virus transmissibility.
Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants.
PMID: 34537361
2022
Clinical microbiology and infection
Method: Using a 1-step protocol, cDNA was prepared from the RNA extracts and amplified on a LightCycler 480II (Roche Diagnostics, Rotkreuz, Switzerland) applying VirSNiP SARS-CoV-2 Spike N501Y, del H69/V70 (DeltaH69-V70), E484K, H655Y, L452R and P681R probe kits (TIB Molbiol, Berlin, Germany) followed by PCR melting curve analysis using the LightCycler 480 SW1.5.1 analysis software.
Result: E484K, H655Y,
Result: E484K-, H655Y-, L452R- and P681R-specific PCRs were applied according to the testing algorithm presented in Figure 1 .
SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines.
Introduction: Additionally, P681R mutation at the S1-S2 cleavage site is thought to increase viral replication, leading to higher viral loads and increased transmission.
Table: P681R
Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm.
PMID: 35266951
2022
Genetics and molecular biology
SARS_CoV_2 mutation literature information.
PMID: 
2022
PeerJ
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