Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp.
1Abstract: Second, this pattern was much delayed or even non-existent for the ""mutant"" (MT) strain that harbored both 14408 C>T and 23403 A>G mutations."
Abstract: Among them, 14408 C>T and 23403 A>G mutations in RdRp and S, respectively, became dominant in Europe and the US, which led to debates regarding their effects on the mutability and transmissibility of the virus.
Introduction: In our previous study, where we analyzed 11,208 SARS-CoV-2 genome sequences, we showed that RdRp mutations, particularly the 14408 C>T mutation, were associated with SARS-CoV-2 genome evolution and higher mutation density.
Introduction: In the current study, we analyzed the time-dependent changes in
Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders.
Result: The most frequent haplogroups in Spain were A2a5 (n=354; 38.4% of Spanish haplotypes; diagnostic variants: C241T-C3037T-C14408T-A20268G-A23403G), A2a4 (n=72; 7.8%; diagnostic variants: C241T-C3037T-C14408T-A23403G plus characteristic MNP: GGG28881AAC), A2a10 (n=26; 2.8%; diagnostic variants: C241T-C3037T-C14408T-A23403G-C29144T), B3a (n=278; 30.2%; diagnostic variants: C8782T- PMID: 32937868
2020
Viruses
Result: Mutations C241T, C3037T, C14408T, and A23403G (MP4) provided the basis for the other MPs patterns; meanwhile, mutations G28881A, G28882A, and G28883C appeared together.
Discussion: We found that the basis mutations, which contain C241T, C3037T,
Discussion: et al., but with the additional mutations T265I on ORF1ab, Q57H on ORF3, and the four basic mutations (C241T, C3037T, C14408T, and A23403G).
Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization.
Result: Various studies have demonstrated the SNV C14408T in ORF1b to be associated with a virus subtype found abundantly in New York as well as multiple European countries, which is designated as an ISM hotspot site 8 in Table 1.
A persistently replicating SARS-CoV-2 variant derived from an asymptomatic individual.
PMID: 32967693
2020
Journal of translational medicine
Result: Alignment analyses showed that, with respect to the Wuhan-Hu-1 Reference Genome NC_045512.2, SARS-CoV-UNIBS-2 AP66 consensus sequence displayed 6 nucleotide substitutions (C241T; C3037T; C14408T; T21784G; C21846T; A23403G) leading to 4 non-synonymous changes (ORF1ab polypeptide: P4715L; S protein: N74K, T95I, D614G).
Result: Less pathogenic GZ69 consensus sequence differed from Wuhan-Hu-1 isolate in 11 nucleotide positions (C241T; C2939T; C3037T
Reinfection with SARS-CoV-2 and Failure of Humoral Immunity: a case report.
Result: Conspicuously, the July sequence (InCoV139-July) harbors none of the canonical mutations defining clade 19B and instead shares the canonical mutations defining clade 20A (C3037T, C14408T and A23403G), 1 canonical mutation of clade 20C (G25563T), as well as 1 other 20A mutation.
Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice.
Discussion: Of the 87 sequences that have the D614G mutation, 69 have the C214T mutation, 15 have the C3037T mutation, and 48 have the C14408T mutation.
Discussion: Several other mutations reportedly accompany the D614G mutation on the S gene and include C214T, C3037T, and the C14408T mutations, and together, these form the globally dominant strain of SARS-CoV-2.
SARS_CoV_2 mutation literature information.
PMID: 
2020
PeerJ
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