In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1.
PMID: 34307830
2021
Informatics in medicine unlocked
Introduction: Top variants in the SARS-CoV-2 genome include high-frequency variants including C241T, C1059T, C3037T, C14408T, A23403G, G25563T, and G28883C, out of which the C241T variant had a 99 % frequency with 0.505 entropy by October 2020.
Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia.
Result: There was only one single nucleotide difference of crRNA-0 at 23403 (A>G)
Figure: Synthetic mismatches are placed in -3 to +3 position of the SNP (A23403G) site of D614G mutation.
Figure: The 3' end of the forward primer is located at the SNP (A23403G) site of D614G mutation with a synthetic mismatch which is the same as that of crRNA-1.
Discussion: Therefore, we designed crRNAs with additional nucleotide mismatches from the -3 to +3 positions centered around the A23403G site.
Discussion: When coupled with a synthetic mismatch primer, whose 3' end is located at the D614G SNP (A23403G) site, the D614G mutation was selectively amplified.
Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021.
Result: Three mutations were found in > 95% of the genomes: A23403G (S:D614G), C14408T (ORF1ab:L4715), and C3037T (ORF1ab:F924), which are signatures of the B.1 and derived lineages that spread early in the pandemic.
Result: Excluding the substitution at position 241 in the 5' UTR, the top three most frequent mutations were the C3037T (59.9%), C14408T (59.9%) and A23403G (D614G) (57.4%).
Result: From March to December, substitutions appeared consistently at the genomic positions C241T, C3037T, C14408T and A23403G.
Result: The second LD set comprised C3037T, C14408T and A23403G mutations in viruses isolated from March to December and involving a single synonymous and non-synonymous mutation in ORF1ab, together with a si
An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms.
Result: Synonymous SNPs from this Farm A isolate included C1059T, C3037T, C6336T, G12795A, C14408T, C20930T, A23064C, A23403G, G25563T, C25936T, C28887T, were also identical to those of MW474212 from a human in Washington State.
Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave.
Result: All strains clustered under this group, including those sequenced in the current study, possessed the three GISAID clade G genetic variants, C241T, C3037T, and A23403G with an additional mutation C14408T.
Result: Based on the GISAID clade assignment, the samples detected during early April 2020 (4Apr20-3-Hu/2020 and 5Apr20-64-Hu/2020), and all samples detected in October 2020 (third epidemic wave) denoted clade G (Table 1), possessed genetic variations at C241T, C3037T, and A23403G.
Result: The A23403G was encoded for substitution of aspartic acid with glycine in the S-614 (S-D614G)
Host Response to SARS-CoV2 and Emerging Variants in Pre-Existing Liver and Gastrointestinal Diseases.
PMID: 34760721
2021
Frontiers in cellular and infection microbiology
Introduction: Further, L clade evolved to V (G11083T, G26144T, NSP6-L37F + NS3-G251V) and G (C241T, C3037T, A23403G, and S-D614G); and later G clade evolved into GH (C241T, C3037T, A23403G, G25563T includes S-D614G + NS3-Q57H), GR (C241T, C3037T,
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
Result: The A23403G mutation causes a change from Aspartate (D) to Glycine (G) in protein position 614 (spike protein) which is responsible for the initial entry of the virus through the ACE2 receptor and is associated with the severity of COVID 19.
Figure: The A23403G, C3037T, C14408T, and C241T are the most widespread mutations globally.
Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020.
SARS_CoV_2 mutation literature information.
PMID: 
2021
Informatics in medicine unlocked
Browser Board
Co-occurred Entities
Filtrator
ViMRT