Result: 3) and also two edit events (non-defining amino acid substitutions): L18F and P812L are required to transform variant V1 into V18.
Result: Two edit events: L18F non-defining substitution and deletion of defining S982A substitution are required to transform variant V9 into V22.
Discussion: (1) a bit more distant linkage for variant V18 was also correctly predicted by assigning V18 to cluster C8, such as variant V18 might have evolved (directly or indirectly) from V1 upon substitutions: L18F and P812L.
Discussion: while V22 can be also linked to V9, but two alterations must had happened: L18F non-defining substitution and deletion of S982A defining substitution.
SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern.
PMID: 34468141
2021
Journal of chemical information and modeling
Introduction: This S variant features the additional mutations L18F (in common with P.1) and R246I but does not feature the Delta241-243 deletion, whose existence was still debated when the authors released their study in January 2021.
Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity.
PMID: 34502041
2021
International journal of molecular sciences
Discussion: After Alpha, the second main VOC detected was Beta in October 2020 in the South African population, and it had five main mutations, which were reported to be beneficial for transmission:L18F, K417N, E484K, N501Y and D614G.
Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines.
Method: SARS-CoV-2 neutralizing antibodies were quantified using lentivirus particles that incorporate SARS-CoV-2 S protein (Wuhan-Hu-1 isolate mutated to contain D614G) or the B.1.351 variant S protein (L18F-D80A-D215G- L242- A243- L244-K417N-E484K-N501Y-D614G-A701V) on their surface and express firefly luciferase reporter gene for quantitative measurements of infection by relative luminescence units (RLUs) as described.
In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2.
Method: We used the following amino acids replacements and deletions in Spike for each lineage-based COG-UK defined changes for each lineage; Beta (B1.351; L18F, D80A, D215G, R246L, K417N, E484K, N501Y, A701V), Gamma (P.1; L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y H655Y, T1027I), Alpha (B.1.1.7; Delta69-70, D144, PMID: 34536797
2021
Virology
Result: Our results show that all the NTD mutations, namely L18F, T20N, P26S, D138Y and R190S, attenuated the binding of naive-vaccinated plasma Abs.
Result: While we did not observe a significant decrease in plasma recognition of the B.1.351 Spike, most single mutants of this VOC (L18F, D80A, D215G, Delta242-244, R246I in the NTD, and K417N in the RBD) exhibit decreased binding.
The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages.
Result: An F at residue S/18 is also observed in 10% of other known Sarbecoviruses and the L18F mutation was the 28th most common in sampled SARS-CoV-2 genomes on June 4, 2021.
Result: In addition to the 29 convergent mutations that displayed frequency increases between March 15 and June 1, 2021, the meta-signature includes deletion mutations at ORF1a/3675-3677, S/69-70, S/144, and S/241-243 (which, while displaying convergence between the different 501Y lineages, were not amenable to selection analyses) and the convergent signature substitutions L18F, K417N/K, and N501Y (which were already at high frequencies in multiple 501Y lineages by March 15, 2021).
Result: S/18 falls within multiple different predicted CTL epitopes and the L18F mutation is known to reduce viral
Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants.
Result: The Beta S is comprised of the L18F, D80A, D215G, and 242-244 mutations in the NTD, K417N and E484K mutations in the receptor-binding domain (RBD), and A701V in the S1/S2 cleavage site.
SARS_CoV_2 mutation literature information.
PMID: 
2021
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