Prolonged shedding of infectious viruses with haplotype switches of SARS-CoV-2 in an immunocompromised patient.
PMID: 35430092
2022
Journal of infection and chemotherapy
Conclusion: When haplotype 1 was compared with Wuhan-Hu-1/2019 (GenBank accession number; MN908947), it had ten non-synonymous (ORF1a:Q2702H and S2981F, ORF1b:P314L, T1404 M, P1567L, and R2684I, S gene:D614G, N gene:R203K, G204R, and M234I) and five synonymous mutations.
Role of the Microbiome in the Pathogenesis of COVID-19.
PMID: 35433495
2022
Frontiers in cellular and infection microbiology
Abstract: Soon after the first outbreak due to the wild-type strain in December 2019, a genetic variant D614G emerged in late January to early February 2020 and became the dominant genotype worldwide.
Conclusion: The two most commonly occurring mutations, Spike_D614G and Nsp12_P314L, were structurally modeled, which showed that these mutations had the potential to enhance viral entry and replication, respectively.
Introduction: Among these, the D614G clade was the most common and was first found in late January 2020 in China, according to a study conducted by.
Introduction: Earliest samples from the USA appeared to have been derived from China and belonged to basal or L84S
Table: D614G
Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD.
Abstract: Among them, D614G, B.1.640.1, and B.1.630 formed a cluster, C.1.2 and B.1.640.2 formed a cluster, and BA.1, BA.2, and BA.3 formed a cluster.
Result: Among them, the D614G immunized serum had the strongest neutralization protection to the original
Table: D614G
Discussion: AM180 and 9G11 lost neutralizing activity to the other seven variants except for D614G, presumably due to the E484 mutation.
Discussion: Among them, D614G, B.1.640.1, and B.1.630 formed a cluster, C.1.2 and B.1.640.2 formed a cluster, and BA.1, BA.2, and BA.3 formed a cluster.
Discussion: Our data indicated that D614G, Alpha, Delta, and Mu were similar in immunogenicity, and these sera had significantly reduced protection against Omicron sublineages (Figure S1).
Characteristic analysis of Omicron-included SARS-CoV-2 variants of concern.
Discussion: In July 2020, a strain with the spike protein D614G mutation was discovered in Europe and subsequently became the main form of the virus pandemic.
Discussion: In the Alpha and Omicron strains, two key deletions, H60V70, are on the epitope, which can affect the immune escape of the S protein (Figure 4F), whereas N501Y and D614G have almost no effect on the antigen score, and the P681 mutation slightly reduces the epitope score and may have a certain impact.
Discussion: The RBD regions of Alpha, Beta, Delta, and Omicron strains are more exposed, and the junction between the variants S protein and the virion has a prominent structure, which may be caused by the D614G mutation.
Durability and Cross-Reactivity of SARS-CoV-2 mRNA Vaccine in Adolescent Children.
1Abstract: We tested the durability and cross-reactivity of anti-SARS-CoV-2 serologic responses over a six-month time course in vaccinated adolescents agains
3Introduction: Here, we quantified relative antibody responses in adolescent children immediately following the Pfizer-BioNTech mRNA vaccination and six months post-inoculation and analyzed the efficacy of the humoral response against the D614G (""wild type"") SARS-CoV-2 and latest variant of concern (VOC), Omicron."
4Method: Serological analyses were performed using an in-house enzyme-linked immunosorbent assay (ELISA) that detects IgG against the D614G (""wild type"") SARS-CoV-2 Spike, the D614G (""wild type"") Receptor-Binding Domain (RBD), or the Omicron SARS-CoV-2 VOC RBD by using the previously described method."
Comparative Evaluation of Six SARS-CoV-2 Real-Time RT-PCR Diagnostic Approaches Shows Substantial Genomic Variant-Dependent Intra- and Inter-Test Variability, Poor Interchangeability of Cycle Threshold and Complementary Turn-Around Times.
Abstract: We comparatively assessed the variability of Ct values generated by six diagnostic approaches by testing serial dilutions of well-characterized isolates of 10 clinically most relevant SARS-CoV-2 genomic variants: Alpha, Beta, Gamma, Delta, Eta, Iota, Omicron, A.27, B.1.258.17, and B.1 with D614G mutation.
Introduction: The main aim of this study was to comparatively assess the variability of Ct values generated by six previously thoroughly evaluated rtRT-PCR assays and platforms by testing serial dilutions of well-characterized SARS-CoV-2 isolates of the clinically most relevant genomic variants (Alpha, Beta, Gamma, Delta, Eta, Iota, Omicron, A.27, B.1.258.17, and B.1 with D614G mutation).
Discussion: In addition, variant B.1.258.17 as the main lineage during the second wave, variant A.27 as a rare variant, with mutation N501Y, and variant B.1 (with
Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements.
Result: All B.1.466.2 and B.1.470 variants in Indonesia carried the D614G spike protein mutation, as do the other VoCs (Table 3).
Result: As well as a B.1.1 variant, all 12 genomes share common mutations in the spike protein D614G and NSP12_P323L (Table S1).
Result: In Indonesia, this P323L mutation was found in all B.1.466.2, B.1.1.7, and B.1.617.2 variants (Table 3) and was co-present with the D614G mutation in many genomes in the world.
Highly Thermotolerant SARS-CoV-2 Vaccine Elicits Neutralising Antibodies against Delta and Omicron in Mice.
Result: For monomeric formulations the fold reduction values were 2.5 and 14.4 and for trimeric 3.0 and 16.5, to Delta and Omicron, respectively, compared to VIC31-D614G.
Result: Neutralisation assays were performed using VIC31-D614G, Delta and Omicron SARS-CoV-2 variants.
Result: The mean antibody titres to VIC31-D614G following immunisation with the vaccine formulations comprising antigens presented as monomers (Vaccines 1-3) showed a statistically non-significant (p < 0.1) increase when compared to the trimers (Vaccines 4-6) (Figure 3J-L; Table 3).
Result: The reduction in neutralisation of Omicron was more pronounced, ranging from a 10.1- to 22.0-fold decrease for the six vaccine formulations, when compared to VIC31-D614G and was statistically significant (p < 0.01) for all.
Result: There was a reduction in neutralising tit
Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity.
Introduction: This process is driven by both escape from neutralizing antibodies, where mutations like Method: A QuikChange Lightening Site-Directed Mutagenesis kit was used to generate amino acid substitutions in the pCDNA wild-type spike plasmid carrying a D614G (received from S.
Discussion: These reports demonstrate that spike residues like D614G and N501Y are located at the distal region of the spike RBD and facilitate transitions from a closed to open state of the spike prior to ACE2 binding, enhancing the stability and affinity of the viral spike to its receptor and subsequently affecting viral spread.
Increased resistance of SARS-CoV-2 Lambda variant to antibody neutralization.
Result: Analysis of two other Class 3 antibodies, REGN10987 and S309, showed that neither recognized the L452 and F490 residuals directly but each still neutralized the Lambda variant with similar potencies as those against D614G-WT.
Result: Compared with the WT strain (D614G-WT), both Lambda variant and L452Q/F490S mutated virus reduced the susceptibility by approximately 50%.
Result: SARS-CoV-2 Lambda variant harbored G75V, T76I, R246N, and Delta246-252 mutations in the N terminal domain, L452Q and F490S in the RBD, D614G and T859N
SARS_CoV_2 mutation literature information.
PMID: 
2022
Journal of infection and chemotherapy
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