Arterial and Venous Thrombosis Complicated in COVID-19: A Retrospective Single Center Analysis in Japan.
PMID: 34869681
2021
Frontiers in cardiovascular medicine
Discussion: Recently, several reports described the promotion of thrombus formation via the activation of platelets, the induction of tissue factor, or PAI-1 using virus particle of the Wuhan strain or recombinant S1 protein with D614G single mutation.
SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity.
Introduction: the mutation D614G in the virus spike protein), which tended to be found together, were reported to show significant positive correlations with death, and to be found more frequently in severe cases than mild cases.
Table: D614G
Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure.
Introduction: One of the first variations that spread vigorously across countries was Asp614Gly at the spike protein, with this mutation showing higher viral loads than the reference virus from Wuhan, China.
Table: Asp614Gly
Discussion: A Consurf analysis indicated that all the mutations were located in variable regions of the protein except for Asp614Gly.
Discussion: A comparison of surface hydrophobicity of the trimeric spike reference protein with the Asp614Gly mutation over the simulation trajectory indicated surface hydrophobicity changed for both proteins.
Discussion: On the other hand, the Asp614Gly missense mutation, which has been widely detected in different regions of the world, was seen in two (ACUTG-1 and ACUTG
COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang.
5Result: Based on the Cryo-EM structures, it has been proposed that S-D614G substitution allosterically leads to more ""open"" conformations or a higher percentage of RBD in a ""up"" position that facilitates the interaction of RBD with the ACE2 receptor."
Result: Considering the proximity of N603 to the S-D614G substitution site, the glycan variation on N603 might have similar effect as that on the N616.
Result: One is the adaptability of the N-glycan shielding layer to the structural changes in the original protein caused by the S-D614G substitution.
Result: The closest glycosylation site to the S-
Reduced neutralization of SARS-CoV-2 B.1.617 variant by convalescent and vaccinated sera.
Abstract: Our results showed that, compared to D614G and B.1.1.7 variants, B.1.617 shows enhanced viral entry and membrane fusion, as well as more resistant to antibody neutralization.
Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein.
Introduction: bearing resemblance to previous evolutionary sweeps, including the D614G substitution in 2020, B.1.1.7 (Alpha) last fall and winter, and Delta this spring and summer (GISAID acknowledgment table can be found at doi: https://doi.org/10.1101/2021.09.27.461949).
Emergence of novel combinations of SARS-CoV-2 spike receptor binding domain variants in Senegal.
Introduction: All three of the genomes carrying the L452R/N501Y combination belonged to the A.27 lineage (clade 19B) and did not encode the D614G mutation that predominates most global infections today.
Introduction: In addition to the L452R + N501Y double mutant, a single genome was identified that carried a unique combination of E484K + N501T spike RBD mutations in a B.1 lineage genome (clade 20C) with D614G also present.
Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants.
7Figure: The reference ""wild-type'"" virus B.1 was assumed (with no mutation D614G and other spike protein changes)."
Abstract: The most often observed were positive mutations, especially D614G and E484K, located in the region of S1/S2 junction, and in the receptor-binding domain (RBD), respectively.
Table: D614G
Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021.
Figure: Spike mutations of SARS-CoV-2 Delta variant clinical isolates sequenced in Denmark between 13 March 2020 (D614G) and 12 October 2021, which were used to evaluate virus neutralisation of an early pandemic strain Figure: Dark turquoise boxes indicate Delta lineage-defining spike mutations present in all Delta lineages/sub-lineages evaluated, light turquoise boxes indicate the AY.4 sub-lineage mutation, light cyan boxes indicate the AY.4.2 sub-lineage mutations, patterned boxes indicates other mutations present in the strains evaluated, and grey boxes indicates the D614G mutation that predominated globally since April 2020.
Figure: Fold changes are relative to D614G.
Figure: Fold changes are relative to the early pandemic strain D614G.
COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang.
Introduction: One of the notable variations, the D614G mutation, encodes a change from aspartic acid to glycine in the C-terminal region of the S1 domain of the viral spike protein of SARS-CoV-2.
Introduction: Since late 2020, all emerging variants of concern (VOC) have carried the D614G mutation.
Introduction: This hypothesis is corroborated by in vitro studies which showed that the D614G mutation is correlated with increased infectivity in cell models.
Result: Using the inferred value of sigma = 1.31, we estimated that the D614G mutation would increase the herd immunity threshold from 50% to 62%.
Discussion: Firstly, we only considered the D614G mutation and simply categorised the sequences on GISAID by aligning the spike
SARS_CoV_2 mutation literature information.
PMID: 
2021
Frontiers in cardiovascular medicine
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