Abstract: Nation-wide mutational analysis depicted >0.5 million mutation events with four major mutations in >19,300 genomes, including two mutations in coding (spike (D614G), and NSP 12b (P314L) of rdrp), one silent mutation (NSP3 F106F) and one extragenic mutation (5' UTR 241).
Result: Two mutations in the protein coding region i.e., D614G in spike and P314L in NSP 12b; one extragenic mutation at 241 position of 5'UTR and one silent mutation at F106 NSP3.
Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation.
Figure: (Lower left) The size distributions of plaque-like spots in D614G-infected and D614G/P681R-infected cultures.
Figure: (Right) The size distributions of adherent GFP+ syncytia in the D614G mutant-infected (n = 147) and the D614G/P681R mutant-infected (n = 171) cultures.
Figure: A B.1.617.2/Delta and a D614G-bearing B.1.1 were inoculated in cells, and the copy number of viral RNA in the supernatant was quantified using RT-qPCR.
Figure: A statistically significant difference (*, P < 0.05) versus D614G S was determined by two-sided Student's t test.
Figure: A statistically significant difference versus the D614G
Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France.
Result: Finally, viral neutralisation in the presence of a monoclonal conformation-dependent antibody targeting the spike receptor binding domain led to a 50% reduction in neutralisation of 677H-harbouring spike relative to 677Q-harbouring spike (wild type), and of Q677H/D614G-harbouring spike relative to D614G only-harbouring spike.
A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain).
Abstract: Almost all (96.4%) were carrying D614G mutation in the S protein, with additional mutations that define lineages or variants.
Result: The D614G (96.4%) substitution was observed in most viral genomes, in addition to multiple mutatio
Discussion: Most circulating B-viruses were carrying the amino acid substitution D614G in the Spike, which appeared by the end of March 2020 and is present in most later circulating lineages belonging to GISAID's G clade.
Discussion: This major predominance of variants carrying this mutation was because D614G improves viral infectivity and viral transmission giving an advantage to virus by relaxing the trimeric Spike structure and facilitating the viral entry to the cell, as previously reported.
SARS-CoV-2 Neutralization in Convalescent Plasma and Commercial Lots of Plasma-Derived Immunoglobulin.
Abstract: METHODS: Final containers of IVIG/SCIG and CP donations were analyzed by commercial ELISA for anti-SARS-CoV-2 S1-receptor binding domain (RBD) IgG as well as microneutralization assay using a patient-derived SARS-CoV-2 (D614G) isolate.
Discussion: A further limitation is that the data presented here were generated using the D614G variant close to Wuhan wildtype strain, while the pandemic is currently driven by SARS-CoV-2 variants of concern and interest.
Discussion: While final container neutralization potencies against SARS-CoV-2 (D614G) are strongly increasing, it is of interest how these could translate into anti-SARS-CoV-2 IgG steady-state trough levels in a patient, which is one possible, yet not validated, correlate of immune protection.
Discussion: While neutralizing plasma antibody
Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021.
PMID: 34848355
2022
Infection, genetics and evolution
Result: Among haplotype 2, haplotype 2A with the mutations at nsp12 P323L, Spike D614G, and N R203K, G204R, markedly increased from 9.1% post-6-month spread to 15.23% post-1-year spread, in which sub-haplotypes 2A _1 (13.33%) and 2A_2 (1.90%) belonged to Pangolin lineages B.1.1.7 (WHO label Alpha) and B1.1.519 variants, respectively.
Result: Among the sub-haplotypes of haplotype 2A variants, sub-haplotype 2A_1 was the most prevalent sub-haplotype in the partly vaccinated rate group, containing three mutations in nsp3 (T183I, A890D, I1412T), seven new mutations in PMID: 34871906
2022
Journal of clinical virology
4Method: The following samples were obtained: IC19 (hCoV-19/England/IC19/2020 EPI_ISL_475572 2020-03-17), a B.1 lineage virus with the D614G spike mutation but otherwise the same as the original ""wild-type"" Wuhan virus."
Table: D614G
The significant immune escape of pseudotyped SARS-CoV-2 variant Omicron.
Abstract: Our results indicated that the mean neutralization ED50 of these sera against Omicron decreased to 66, which is about 8.4-folds compared to the D614G reference strain (ED50 = 556), whereas the neutralization activity of other VOC and VOI pseudotyped viruses decreased only about 1.2-4.5-folds.
Introduction: The neutralization sensitivity of PV-Omicron against serum samples from a panel of COVID-19 convalescent patients was tested, using PV-D614G (S protein from SARS-CoV-2 D614G strain) as the reference.
Result: The ED50 of Alpha, Beta, and Gamma is reduced about 1.2, 2.8, and 1.6-fold, respectively, compared to the reference strain PV-D614G (Figure 1B-D), while the reduction of neutralization for Lambda and Mu variants is 1.7- and 4.5-fold, respectively (Figure
Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform.
Abstract: We used a Cas12a-based RT-PCR combined with CRISPR on-site rapid detection system (RT-CORDS) platform to detect the key mutations in SARS-CoV-2 variants, such as 69/70 deletion, N501Y, and D614G.
Introduction: Because the
Figure: (A) D614G detection of SARS-CoV-2 variants using the RT-CORDS paper strip assay.
Figure: (B, C, D) in vitro cleavage assay of N501Y, D614G and 69/70 deletion targets using Cas12a/crRNA-W and Cas12a-crRNA-M.
Figure: (E, F) Sensitivity of D614G detection using the RT-CORDS lateral flow strips system.
Figure: (E, F, G) Identification of N501Y, D614G and 69/70 deletion targets through CRISPR/Cas12a trans-cleavage of the fluorescence reporter.
A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients.
Introduction: They reported that S mutation D614G increases infectivity.
Discussion: Also, there were two other sequences sampled from Shiraz in January 2021, which had five specific mutations as indicator of the Alpha variant (D614G, H69del, N501Y, V70del, Y144del) and were clustered along with the Alpha variants in phylogenetic tree; however, these sequences did not contain the other specific mutations of Alpha variant including A570D, D1118H, L699I, P681H, S982A and T716I.
SARS_CoV_2 mutation literature information.
PMID: 
2022
Virus research
Browser Board
Co-occurred Entities
Filtrator
ViMRT