literature

SARS_CoV_2 mutation literature information.

Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations.

PMID: 34458642 2021 Heliyon

Abstract: The most frequent mutation that occurred in 98% isolates was 3037C>T which is a synonymous change that usually accompanied 3 other mutations that include 241C>T, 14408C>T (P323L in RdRp) and Table: 23403A>G

Discussion: Those mutations include 3037C>T (98%), 14408C>T (98%) and 23403A>G (97%) where the last two are non-synonymous mutations (P4715L in ORF1ab or P323L in RdRp and D614G in Spike protein).

AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus.

PMID: 34512928 2021 Computational and structural biotechnology journal

Introduction: In our previous work, we found 9 candidate key mutations, including Result: For the UK, the 5 of 6 haplotypes (including H1-1-1, H1-2-1, H1-4-1, H1-4-2, and H1-4-3), which derived from H1 with previous 4 specific mutation sites (C241T, C3037T, C14408T, and A23403G), accounted for 91.95% of the population (Table 4).

Result: H1-3-2 had previous 5 specific sites (C241T, C3037T, C14408T, A23403G, and G25563T) and C1059T (Table 5, Table 6), which had a stable prevalent trend between December 01, 2020 and February 02, 2021 in the USA.

Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis.

PMID: 34514180 2021 Heliyon

Result: The sequencing results showed and confirmed the HRM analysis that all samples were identified as G614 variant by the presence of missense mutation A to G at position 23403 (NCBI Reference Sequence Wuhan-Hu-1/NC_045512.2 = 23403A > G) which causes changes in the amino acid, Aspartic Acid (D) into Glycine (G) at the Spike residue 614 (D614G) (Figure 3).

Discussion: The G614 variant carried the missense mutation 23403A > G (Reference Sequence = NC_04512.2), which allowed the higher melting temperature, as Guanine (G) base needs 3 hydrogen bonds to form a base pair, whereas Adenine (A) base needs only 2 hydrogen bonds.

Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia.

PMID: 34540148 2021 Iranian journal of microbiology

Table: A23403G

Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time.

PMID: 34540874 2021 Frontiers in medicine

Result: We found (Table 1) that during the first epidemic wave, all viruses derived from the Wuhan-Hu-1 reference strain but carried the non-synonymous A23403G mutation, leading to the substitution D614G in the spike.

Table: A23403G

Discussion: A major characteristic of the African isolates was the high frequency (84.2%) of the A23403G mutation leading to a D614G.

Complete genome sequencing and molecular characterization of SARS-COV-2 from COVID-19 cases in Alborz province in Iran.

PMID: 34549097 2021 Heliyon

Result: The sample AK-SARS-27 had only one SNV (23403A > G) which corresponded to the missense change D614G.

Discussion: Only one of the sequenced genomes had the SNV 23403A > G which results in D614G amino acid substitution, but it was not accompanied by three other mutations which are always co-occurring in the same genome.

Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure.

PMID: 34578142 2021 Pathogens (Basel, Switzerland)

Result: Clade 20A defined by C14408T (Nsp12/RdRp) and A23403G (S: D614G) was seen in 58% of the samples, clade 19A defined by positions 8782C (Nsp3) and 14408C (Nsp12/RdRp) was seen in 38% and 20B denoted by positions C3037T (Nsp3: 106F); A23403G (S: D614G); C14408T (Nsp12/RdRp: P4715L) and G28881A and

Development of a PDRA Method for Detection of the D614G Mutation in COVID-19 Virus - Worldwide, 2021.

PMID: 34594910 2021 China CDC weekly

Method: A forward primer and two specific reverse probes for A and G nucleotides of A23403G polymorphism were designed using Oligo7 software.

Method: The PDRA assay included two real-time RAA reactions (A and G) to detect the A and G nucleotides of the D614G mutation (A23403G polymorphism), respectively.

Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus.

PMID: 34637920 2021 Infection, genetics and evolution

Result: The SS4 cluster carried the signature mutation C241T, C3037T and A23403G.

Table: A23403G

Discussion: Noteworthy, important mutations contributing to the evolutionary success to some strains (i.e., with A23403G) were not present in these unclassified clusters.

Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model.

PMID: 34676891 2021 Journal of medical virology

Introduction: Yin reported that the 5'-untranslated region (5'-UTR) mutation 241C>T is co-occurring with three other mutations, 3037 C>T (NSP3: C318T), 14408C>T (RdRp: p.P323L), and 23403A>G (S: p.D614G).

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