Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India.
PMID: 35427787
2022
Infection, genetics and evolution
Abstract: First, we served comparative genomics, such as genome sequence submission patterns, mutational landscapes, and structural landscapes of significant mutations (N501Y, D614G, L452R, E484Q, and P681R).
Abstract: The structural pattern was analyzed in the N501Y, D614G L452R, E484Q, and P681R mutations.
Result: Again, like the previous point AA mutation, we also evaluated the D614G mutation, which was identified as the B.1.1.7 variant.
Result: In the D614G structure, the amino acid changed from Asp614 Gly.|mg
Split T7 promoter-based isothermal transcription amplification for one-step fluorescence detection of SARS-CoV-2 and emerging variants.
Conclusion: Finally, (v) broad applicability was verified through the multiplex detection of the SARS-CoV-2 variants (D614G mutation) as well as through the direct detection of bacterial 16S rRNA without the need for additional nucleic acid purification.
Introduction: D614G), conferring greater infectivity and more rapid spread, have become predominant in various regions.
Introduction: Moreover, STAR was utilized for multiplex detection of the D614G mutation and N gene of SARS-CoV-2 in a single tube as well as for the direct detection of bacterial 16S rRNA without additional nucleic acid purification, thereby confirming the wide applicability of this method for nucleic acid biomarker detection.
Result: 5B indicate that G at N4 minimized the background noise in the presence of the wild-type target while generating a high fluorescence sign
Efficacy of vaccination and previous infection against the Omicron BA.1 variant in Syrian hamsters.
Introduction: Here, in the hamster model, we addressed these issues under controlled conditions using the Omicron variant and isolates that are no longer circulating in nature (i.e., a Wuhan-like isolate and an isolate with only a D614G spike mutation).
Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution.
PMID: 35419205
2022
Evolution, medicine, and public health
Abstract: Methodology: We performed experimental evolution with two strains of SARS-CoV-2, one carrying the originally described spike protein (CoV-2-D) and another carrying the D614G mutation that has spread worldwide (CoV-2-G).
Conclusion: Assuming that the D614G genotype is better adapted than its ancestor in Vero cells, this observation is consistent with the hypothesis that fitter genotypes adapt at a slower pace.
Conclusion: Here, we followed the evolution in cells of two strains of SARS-CoV-2: one with the original spike protein (CoV-2-D) and one carrying the D614G mutation (CoV
Result: This D614G mutation in the spike protein emerged early in the pandemic, increased the infectivity of the virus and became prevalent worldwide.
Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern.
Method: On deep sequencing following amino acid changes were found in the isolate.(NSP5_P132H,Spike_T95I,Spike_K417N,Spike_S373P,Spike_Q493R,Spike_N969K, Spike_H655Y,Spike_N856K,N_R203K,Spike_S371L,NSP3_A1892T, PMID: 35403837
2022
Advanced science (Weinheim, Baden-Wurttemberg, Germany)
Abstract: Pseudotyped and authentic virus-based assays show that COVID-HIG displays broad-spectrum neutralization effects on a wide variety of SARS-CoV-2 variants, including D614G, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Kappa (B.1.617.1), Delta (B.1.617.2), and Omicron (B.1.1.529) in vitro.
Inhibitor screening using microarray identifies the high capacity of neutralizing antibodies to Spike variants in SARS-CoV-2 infection and vaccination.
Abstract: In addition, similar results were obtained using a SARS-CoV-2 pseudovirus neutralization assay specific for wild-type S and five prevalent S variants (D614G, B.1.1.7, B.1.351, P.1, B.1.617.2), thus demonstrating that high antibody diversity is associated with high NAb titers.
Result: Consistent with the observation that the trimerized form of the D614G S protein has an increased binding affinity to ACE2, we also found the D614G mutation modestly improved the binding of S-ACE2 in this study.
Result: Like the convalescent COVID-19 patients, the D614G variant did not alter the neutralizing effect of the NAbs compared to wild-type S1+S2, S2, and PMID: 35398519
2022
Clinical immunology (Orlando, Fla.)
Introduction: Even in the early stage of the pandemic, the D614G mutation increased and replaced the previous strain within a few months; however, since this mutation was outside the RBD, it did not h
Result: Because variant strains such as Alpha variant have been reported in Japan since January 2021, and because this study used samples from patients who had been infected by COVID-19 before that time, all patients were thought to be infected with the Wuhan-hu-1 strain or the strain with D614G.
Discussion: There are several limitations in this study: first, because most of the participants were infected by the Wuhan-hu-1 strain with or without D614G mutation, we cannot assess immune evasion among other strains, such as the neutralization titers of the Delta variant after infection with the Alpha variant.
The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia.
Discussion: Although not associated with worse disease severity, the S_D614G change has been implicated in enhanced transmission and higher viral loads .
Discussion: For Delta variants, we observed 12 key amino acid changes in spike protein that were mostly similar to other studies, including S_T19R, S_T95I, S_G142D, S_E156-, S_F157-, S_R158G, S_K417N, S_L452R, S_T478K, S_D614G, S_P681R, and S_D950N .
Discussion: On the other hand, substitutions in the region encoding the spike protein in Indonesian lineages mainly consisted of thr
SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study.
Figure: (A) Neutralising antibody titres against the original SARS-CoV-2 strain from Wuhan, China (IPBCAMS-WH-01/2019, number EPI_ISL_402123), and the D614G, beta (B.1.351), and delta (B.1.617.2) variants in 141 patients.
Figure: Humoral and cellular immune responses to the original SARS-CoV-2 strain, and the D614G, beta, and delta variants, in recovered patients 12 months after infection.
Discussion: Both the D614G and the delta variants escape from the neutralising antibodies against the original strain, an effect that depends on neutralising antibody titres.
Discussion: However, higher neutralising antibody titres against the original strain contributed to the protection from infection of D614G and delta variants in vitro.
Discussion: However, the D614G variant enhances infectivity mainly
SARS_CoV_2 mutation literature information.
PMID: 
2022
Infection, genetics and evolution
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