Result: Other mutations in IDRs of S, for example, C21575T (L5F), G25049T (D1163Y), G25062T (G1167V), are located nearby N-linked glycan sites (11, 1, and 5 residues, respectively).
Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models.
Result: The hypermutable site at 21575 corresponds to Leu5Phe and the heteroplasmy at 21570 to a Val3Gly; both are located in the signal peptide (SP) in the N-terminal domain of the S protein.
CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention.
Abstract: Our analysis of 1000 S protein sequences from field isolates collected globally over the past few months identified three recurrent point mutations including L5F, D614G and G1124V.
Introduction: In addition, our analysis using a large number of S protein sequences derived from SARS-CoV-2 genomes revealed important mutations including L5F, D614G and G1124V that are although less likely driven by seasonal CoV derived cross-reactive CD8 T cells, may differentially impact CD8 T cell epitope generation by different HLA alleles.
Result: Although we identified major mutations on CD8 T cell epitopes including L5F, D614G and PMID: 32577641
2020
bioRxiv
Result: First, we investigated Sarbecovirus conservation of 14 amino acids in the spike protein in which mutations appear to be accumulating in the SARS-CoV-2 population, namely D614G, L5F, L8V/W, H49Y, Y145H, Q239K, V367F, G476S, V483A, V615I/F, A831V, D839Y/N/E, S943P, P1263L.
Result: In contrast, L5F, L8V/W, H49Y, PMID: 32818213
2020
Research square
Result: We found that the other high frequency S protein mutation L5F is independent of mutation D614G.
The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity.
Result: Notably, single D614G and combined variants with D614G (D614G+L5F, D614G+V341I, D614G+K458R, D614G+I472V, D614G+D936Y, D614G+S939F, and D614G+S943T) demonstrated increased infectivity compared to the reference strain in all the four cell lines (Figures 3A-3D), whereas no difference was found between single D614G and D614G combined variants, suggesting that the en
Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus.
Method: A recurrent amino acid change like L5F (Figure 7) could potentially result from a recurrent sequencing or sequence processing error, or alternatively, it may be of particular interest if it is naturally recurring homoplasy.
Result: The mutation resulting in the signal peptide L5F change recurs many times in the tree and is stably maintained in about 0.6% of the global GISAID data.
Figure: L5F recurs throughout the tree and is often clustered in small local clades.
SARS_CoV_2 mutation literature information.
PMID: 
2021
Journal of medical virology
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