Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm.
PMID: 35266951
2022
Genetics and molecular biology
Result: Haplotypes 5 and 23 (H_5 and H_23, Figure S1 A) have the selected sites A845S and L5F in the S.
Result: Table 4 shows the sites that met these criteria in both datasets [Gamma and Gamma/P1.1/P.1.2; S (L5F, T572I, A845S), ORF3 (L83F, K16N, L85F, D27Y), ORF1a (G150S
An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern.
Result: Of the 93 substitutions that were present in 2020, 61 were no longer present during March 2021 (Figure 5C), and only 8 were present in >5% of samples during March 2021 (NSP2:T85I, NSP12:P323L, S:L5F, S:D614G, NS3aQ57H, NS8:S24L, N:R203K, and N:G204R).
Analysis of SARS-COV2 spike protein variants among Iraqi isolates.
Abstract: Twenty-two distinct mutations were identified within the spike protein regions which were: L5F, L18F, T19R, S151T, G181A, A222V, A348S, L452 (Q or M), T478K, N501Y, A520S, A522V, A570D, S605A, D614G, Q675H, N679K, P681H, T716I, S982A, A1020S, PMID: 34801754
2022
Infection, genetics and evolution
Result: In addition to the mutations previously mentioned and the quickly increasing prevalence of mutations associated with the Alpha variant in the last few months of the analysis, the heatmap reveals four additional mutations that appear to be increasing in prevalence with time (L5F, S98F, A262S, and
Result: first detected in New York (L5F, T95I, D253G; E484K or S477N; D614G, and A701V), appear together consistently after the week of October 4th, 2020, though the fact that many of these mutations are shared with other phylogenetic lineages makes it difficult to conclude that the variant originated at this time point.
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: Haplotype 2B containing the mutations at nsp12 P323L, Spike D614G, ORF3a Q57H, and nsp2 I85I emerged post 6-month spread, evolved into five sub-haplotypes, such as additional mutations at nsp3 K837N, spike protein D80A and D215G in sub-haplotype 2B_1, spike L5F, T95I, D253G in sub-haplotype 2B_4, and spike
SARS-CoV-2 phase I transmission and mutability linked to the interplay of climatic variables: a global observation on the pandemic spread.
PMID: 35028838
2022
Environmental science and pollution research international
Introduction: Apart from this, L5F was also observed in 37 countries; Q239K, V483A, and D839Y/N/E in Europe; G476S and V483A in the USA; and P1263L in the UK.
Dynamics of SARS-CoV-2 Alpha (B.1.1.7) variant spread: The wastewater surveillance approach.
Result: Seven of these mutations (L5F, T73A, S98F, S155I, L216F, D253N and D290Y) were located in the amino terminal domain (NTD) of the spike glycoprotein S, two (S477N and A522S) were located in the receptor binding domain (RBD), and nine (G669V, A706V, K854N, S940A, Q1071L, H1083R, D1084R, <
Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy.
PMID: 35189404
2022
Infection, genetics and evolution
Result: Four major SNVs were identified in single patients: 3157C > T (A964A) in the ORF1ab, 21,575C > T (L5F) in the S gene, 26555 A > G (E11E) and 26,774 G > T (M84I) in the M gene.
Result: Haplotype Hap C was characterized by SNV 21575C > T (L5F) in the S gene while haplotype Hap C.1 was characterized by SNVs 21,575C > T (L5F) in the S gene and C1684T (I473I
Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes.
Result: Interestingly, the mutation Spike:L5F (C21575T), which characterized the viral haplotype of two subjects in Vo', emerged from January 2021 to August 2021 as part of the mutation pattern defining the B.1.526 lineage (Iota variant), prevalent in the USA (Figure S2).
Result: Studies on Spike:L5F highlighted the increase in the protein folding and assembly of virions, as well as the increase in CD8 T cell recognition and killing.
Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach.
Introduction: The Iota variant has six mutations on the spike gene (L5F, T95I, D253G, E484K, D614G, and A701V), whilst the Lambda variant is characterized by seven mutations on the same gene (G75V, T76I, del246/252, L452Q, F490S, D614G, and T859N).
SARS_CoV_2 mutation literature information.
PMID: 
2022
Genetics and molecular biology
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