Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations.
PMID: 34801754
2022
Infection, genetics and evolution
Result: A comparison of the secondary structure of
Discussion: D614G has also been observed to co-occur with Nsp12: P323L, the most common mutation observed in Nsp12.
Discussion: The study validated previous findings of the predominance of spike: D614G and Nsp12: P323L in the population while uncovering recent increases in the prevalence of new mutations in Nsp12 and the spike protein.
Discussion: The very high prevalence of the D614G mutant in the sequences sampled reflects studies documenting increased viral counts in-vitro as well as higher viral loads in infected individuals.
Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein.
Result: Both the S1 and S2 glycoproteins of the wild-type and D614G SARS-CoV-2 strains migrated faster when expressed in the GALE/GALK2 293T cells compared with the migration of these glycoproteins expressed in 293T cells.
Result: Both the wild-type SARS-CoV-2 S glycoprotein and the prevalent D614G variant S glycoprotein were expressed in 293T cells and in the GALE/GALK2 293T
Figure: (A) The wild-type SARS-CoV-2 S glycoprotein (D614, with an aspartic acid residue at 614) and the D614G variant (G614, with a glycine residue at 614) were expressed in wild-type 293T cells (wt) or in GALE/GALK2 293T cells (ko).
Figure: Characterization of wild-type and D614G S glycoproteins in GALE/GALK2 293T cells.
Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination.
Result: In addition, the seven mAbs MWF, A001, CB6, X604, 9A8, M128, and 4E5 did not differ more than 4-fold in their neutralization of the Lambda variant compared with their neutralization of D614G, indicating that these seven mAbs provided good protection against the Lambda variant.
Result: No significant changes existed in the Lambda variant's ability to infect these four cell lines compared with the D614G pseudovirus.
Result: The neutralizing effect of the five Ad5 adenovirus-vectored vaccine-immunized sera against the Lambda variant decreased by an average of 2.5-fold, but this was not statistically different from the effect observed against D614G because of the large differences between samples (Figure 5D, H).
Result: To study the Lambda variant and each individual amino acid mutation's effect on viral function, we constructed 10 pseudovirus strains using the pseudo
Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study.
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.
Method: A B.1.617.2/Delta isolate (strain TKYTK1734; GISAID ID: EPI_ISL_2378732) and a D614G-bearing B.1.1 isolate (strain TKYE610670; GISAID ID: EPI_ISL_479681) were isolated from SARS-CoV-2-positive individuals in Japan.
Method: A plasmid expressing the SARS-CoV-2 S D614G/P681R mutant was generated by site-directed mutagenesis PCR using pC-SARS2-S D614G as the template and the following primers: P681R Fw, 5'-CCAGACCAACAGCCGGAGGAGGGCAAGGTCT-3' and P681R Rv, 5'-AGACCTTGCCCTCCTCCGGCTGTTGGTCTGG-3'.
Method: For the clinical isolates (a B.1.617.2/Delta isolate (strain TKYTK1734; GISAID ID: EPI_ISL_2378732) and a D614G-bearing B.1.1 isolate (strain TKYE610670; GISAI
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).
Result: The D614G (96.4%) substitution was observed in most viral genomes, in addition to multiple mutations defining lineages, such as the mutation set Delta69-70, Delta144, N501Y, A570D, P681H,
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.
Method: SARS-CoV-2 D614G (Human 2019-nCoV ex China_BavPat1/2020_Germany ex China, GISAID ID: EPI_ISL_406862) was kindly provided by Prof.
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-SA
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."
SARS_CoV_2 mutation literature information.
PMID: 
2022
Infection, genetics and evolution
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