Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning.
PMID: 34812411
2021
Informatics in medicine unlocked
Introduction: For instance, the D614G mutation in spike protein was figured out to be increasing in frequency in April 2020 and to have emerged several times globally.
Introduction: Several studies documented that
Result: Furthermore, the monthly basis of sequence analysis revealed that D614G (spike protein), F106F (NSP3), P314L (NSP12b), and 5' UTR:241 mutations are at the top of the mutation analysis chart of every month from March 2020 to December 2020.
Figure: The D614G, F106F, P314L, and C241T are the most widespread mutations globally.
The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice.
Method: In accordance with previous findings, we also identified LG_1 (D614G), LG_2 (L84S) and LG_3 (R203K/G204R).
Method: There is no linkage disequilibrium between D614G and R203K/G204R (rho2 = 0.043, Table S1B), suggesting the independence in evolution between R203K/G204R and D614G.
Result: Correlation analyses of IF tracks between pairs of mutants in these three time intervals show that the evolution of R203K/G204R is independent of that of D614G (Figures S2A-S2D; for details, see STAR Methods).
Result: These
Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India.
Result: Except for the D614G mutation in the Spike protein, which is the defining feature of the B.1 lineage, no mutation was found to be shared between kappa and alpha variants.
Discussion: Of the 14 non-synonymous mutations observed across the genome of all the strains belonging to the kappa variant, five are found in the spike protein (E484Q, L452R, P681R, D614G, Q1071H) and among them the first two lie in the receptor binding domain (RBD) and the third one is adjacent to the furin cleavage site (Figure 7).
A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue.
Result: After the post-infection treatment, curcumin exerted an antiviral effect against SARS-CoV-2 D614G strain at 10 microg/mL of 84.4%, p = 0.0095, and at 5 microg/mL of 31.7%, p = 0.0095 (Figure 5).
Result: As can be seen from Figure 6, the viral titer of D614G strain was significantly reduced through co-treatment strategy (incubation of curcumin with the virus prior to infection) at 10 (92%, p = 0.004), 5 (60.4%, p = 0.004), and 2.5 microg/mL (39.3%, p = 0.004) of curcumin (Figure 6).
Result: By pre-post infection treatment (cells treatment with curcumin, prior and post to infection with SARS-CoV-2) curcumin exerted antiviral activity of 99.0% (p = 0.0095), 51.3% (p = 0.0095), 22.2% (p = 0.0095), and 27.8% (p = 0.0095) against SARS-CoV-2 D614G strain at concentrations of 10, 5, 2.5, and 1.25 microg/mL, respectively (Figure 3).
Result: Curcumin Inhibited SARS-CoV-2
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a Dog in Connecticut in February 2021.
Abstract: It contained both the D614G in spike and P323L in nsp12 substitutions, which have become the dominant mutations in the United States.
Result: The D614G and P323L occurred in China on 24 January 2020 and in the U.K.
Result: The B.1 and its sub-lineages that carry both D614G in spike and P323L in nsp12 substitutions have become the dominant variants across the world.
Result: We found amino acid substitutions in Spike (D614G), N (D377Y, P67S
High Individual Heterogeneity of Neutralizing Activities against the Original Strain and Nine Different Variants of SARS-CoV-2.
Method: Eleven patients were infected by spike D614G-harbouring B lineage strains that spread during the first wave of COVID-19 infections in France, 9 were infected by the Marseille-4/B.1.160 variant, 10 were infected by the Alpha variant, and 12 were infected by the Beta/B.1.351.2 variant.
"Macrophages and Monocytes: ""Trojan Horses"" in COVID-19."
Abstract: We aimed to explore whether variants of SARS-CoV-2 (Chinese-derived strain (D614, lineage A), Italian strain PV10734 (D614G, lineage B.1.1) and Alpha strain (lineage B.1.1.7)) were able to infect monocytes (MN) and monocyte-derived macrophages (MDM) and whether these infected cells may, in turn, be vectors of infection.
Method: SARS-CoV-2 strains, including the wild type Chinese-derived strain (D614, lineage A), Italian strain PV10734 (D614G, lineage B.1.1) and Alpha variant (lineage B.1.1.7), were isolated at 33 C from infected patients' nasal swabs in the permissive VERO E6 (VERO C1008 (Vero 76, clone E6, Vero E6; ATCC1CRL-1586TM) cell line.
The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City.
Discussion: Importantly, they also inferred that the Pro323Leu mutation occurred on an Asp614Gly background.
Discussion: They identified that the Pro323Leu mutation in the RNA-dependent RNA polymerase led to the rapid spread of the virus, rather than the previously reported Asp614Gly mutation in the spike glycoprotein.
SARS_CoV_2 mutation literature information.
PMID: 
2021
Informatics in medicine unlocked
Browser Board
Co-occurred Entities
Filtrator
ViMRT