The Impact of Mutations on the Pathogenic and Antigenic Activity of SARS-CoV-2 during the First Wave of the COVID-19 Pandemic: A Comprehensive Immunoinformatics Analysis.
Abstract: We observed 3362 non-redundant sequences per protein on average within this corpus and described key D614G and N501Y variants spatiotemporally in the initial genome corpus.
Introduction: Additionally, several variants of SARS-CoV-2 genomes have emerged, including the D614G variant, which appeared earlier in the pandemic, or the more recent B.1.1.7 (Alpha) or B.1.617.2 (Delta) variants, which represent the majority of new cases in the U.S.A.
Introduction: Furthermore in a targeted analysis, we achieved greater than 97.9% sequence identity in spike glycoprotein domains and tracked the emergence of the D614G and N501Y spike glycoprotein variants over time and by region of exposure.
Result:
SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity.
Result: A further reduction in neutralization titers was seen against pseudoviruses bearing both L452R and T478 substitutions in RBD displayed (GMT 192) compared to WT(D614G) (GMT 392).
Result: A modest 1.8-fold reduction in titers against C.37 pseudoviruses was observed compared to WT(D614G) pseudoviruses (GMT titers 222 and 392, respectively).
Result: A prior study showed that convalescent sera and vaccine-elicited antibody neutralization titers against pseudoviruses bearing spikes containing L452R-E484Q-P681R substitutions displayed 2-5-fold reduction, compared to the neutralization titers against WT(D614G) pseudoviruses.
Result: Again, pseudoviruses
Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket.
Method: Pymol mutagenesis wizard was used to model Q675H and D614G for both wild-type (wt) and mutant systems.
Result: In particular, in B.1.438.1, B.1.438.2, B.1.438.3, and B.1.1.385 lineages, Q675H and D614G are the sole mutations located in the spike protein.
Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing.
Abstract: Seven compounds reduced weight loss and promoted weight regain of hamsters infected not only with the original strain but also the D614G variant.
A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants.
Method: The fold change of the mutant spike relative to WT D614G in binding or neutralization was calculated by simple division of the respective IC50 or MFI values.
Figure: (C-E) The relative mean fluorescence intensity (MFI) of mAbs or ACE2 binding was determined by comparing the total MFI in the selected gate between the spike variants and WT D614G.
Figure: The IC50 of antibodies against WT D614G are listed in (A).
Figure: Values indicate the fold changes in half-maximal inhibitory concentrations (IC50) (A) and the mean fluorescence intensity (MFI) relative to that of wild-type (WT) D614G (B).
SARS-CoV-2 Variants: Mutations and Effective Changes.
PMID: 34975266
2021
Biotechnology and bioprocess engineering
Abstract: Certain mutations (D614G, E484K, N501Y, K417N, L452R and P681R) have appeared across several different strains, often accompanied by others that may be complementary working together to confer increased infectivity, fitness, or resistance to neutralization.
Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment.
Conclusion: The highly prevalent 23403A>G (p.D614G) variant in the European population ma
Discussion: A recent report corroborated our findings of high prevalence of D614G in Europe.
Discussion: However, given the small sample size, it is hard to ascertain whether D614G is the dominant strain in these countries.
Discussion: In addition to the Netherlands, Switzerland, and France, our data indicate that the D614G sub-strain is frequently detected in Brazil, Finland, and Belgium.
Discussion: Intriguingly, in our data the D614G variant was detected only in 2 out of 151 Chinese patients analyzed.
Discussion: Notably, these two samples do not share common variants besides p.D614G.
A Novel Synonymous Mutation of SARS-CoV-2: Is This Possible to Affect Their Antigenicity and Immunogenicity?
Abstract: These two subtypes were divided by a novel synonymous mutation of D614G.
Introduction: If the mutation of D614G plays a crucial role in the positive selection process, SARS-CoV-2b will be the dominant type of SARS-CoV-2 in the future.
Introduction: Since no amino acid changes were found in this area other than the change of D614G, it is believed that this amino acid change alters the conformation of these immunogenic determinants; consequently, this region is expected to no longer act as a B-cell epitope in SARS-CoV-2b.
Introduction: The results of the antigenic index analysis showed severely reduced indexes of amino acids 615-617 in the SARS-CoV-2b strains compared to SARS-CoV-2a; it is predicted that the change of D614G affects the antigenicity of this region (Figure 1F).
SARS_CoV_2 mutation literature information.
PMID: 
2021
Vaccines
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