literature

Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines.

PMID: 34508827 2021 Biochimie

Method: The chosen sequences of single mutations included the following amino acid substitutions: L5F, L18F, D80A, S98F, A222V, A262S, P272L, K417 N, N439K, L452R, Y453F, S477 N, E484K, E484Q, N501T, N501Y, E583D, D614G, Q675H, Q675P, Q677H,

PMID: 34700382 2021 mBio

Result: Dual mutants containing D614G and other amino acid changes, including those under positive selection or observed in VOCs (L5F, L18F, S98F, W152L/C, E154K, L222V, and A262S in S1-NTD; N439K, L452Q/R, S477N, L478R/K, E484K/Q, N501Y, and A570D within S1-RBD; Q677H/P and P681H/R in S1-CTD; T716I,

Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan.

PMID: 34726786 2021 Journal of medical virology

Abstract: Notably, two rare mutations (E484Q and L5F) were found in the delta variant.

Result: Another distinct and rare spike mutation (L5F [21575 C>T]) was also reported in one 40-year female patient (GISAID ID: EPI_ISL_2894977).

Discussion: Moreover, in one female patient, a less prevalent spike mutation (about 0.5%), L5F was observed.

CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern.

PMID: 34787487 2021 Microbiology spectrum

Method: The SARS-CoV-2 target sequences include (i) the wild-type (WT) gene fragment of S protein (S; nucleotides [nt] 21,563 to 25,384; GenBank accession number MN908947); (ii) the mutant gene fragments of S protein, including mutations L5F, D80A, D215G, R246I, K417N, L452R/Q, Y453F, T478K, E484Q/K, N501Y, A570D, D614G, P681H, A701V, T716I,

A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features.

PMID: 34806033 2021 Current research in structural biology

Introduction: The lineage B.1.526 is classified as a Variant of Interest (VOI) which have multiple spike mutations with unique substitutions L5F, T95I, and, D253G, which were not present earlier in any other lineages.

Result: In early pandemic, L5F substitution in the signal peptide was present, alongwith D614G mutation in the linker.

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

Abstract: Conversely, D3L, L5F, and S97I were found to largely increase the structural stability of the corresponding proteins.

Result: Conversely, 3 missense mutations (D3L, L5F, and S97I) were found to largely increase (DDG value > 0.5) the structural stability of the corresponding proteins.

Result: Mutations [L5F, and R80I], S97I, and [L46C, V48G, G49I, Q57H, W131R, G172V, Q185H, and Y206S] were ident

Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia.

PMID: 34905574 2021 PloS one

Table: p.L5F

Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing.

PMID: 34960813 2021 Viruses

Result: The same minority variants were detected with both protocols in three samples and the resulting percentages were quite similar (L5F: 46.4% with PacBio and 25.6% with Illumina; L176F: 22.6% with PacBio and 37.5% with Illumina; and 27.4% with PacBio and 31.2% with Illumina).

Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India.

PMID: 35017872 2021 Journal of global infectious diseases

Discussion: Besides, D614G in combination with other mutations such as D614G+L5F (n = 23), D614G+V341I (n = 1), D614G+D936Y (n = 3), D614G+S939F (n = 9) and D614G+S943T (n = 2) in strains of the present study was demonstrated to have increased infectivity compared to Wuhan-1 strain.

In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms.

PMID: 34248922 2021 Frontiers in microbiology

Discussion: Following the Cluster 5 discovery, a mink-associated SARS-CoV-2 variant with six spike protein changes appeared (L5F, DeltaH69/V70, Y453F, D614G, N751Y, and C1250F).