Emergence of a second SARS‐CoV‐2 variant with a tremendous genetic leap from its ancestors

Journal of Medical Virology, Journal Year: 2023, Volume and Issue: 95(10)

Published: Oct. 1, 2023

The on-going emergence of the Omicron BA.2.86 variant is one major events in SARS-CoV-2 genetic evolution that remain enigmatic regarding overall virus mutation rate, together with initial variant, BA.1. Indeed, genomes lineage, an offspring second subvariant, BA.2, harbor 39 additional mutations spike compared to this ancestor. Here we comment on phylogeny BA.2.86, positions, and frequencies other SARS-CoV-2, its spike, structural model protein concentrates most mutations.

Language: Английский

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Characterization and Fluctuations of an Ivermectin Binding Site at the Lipid Raft Interface of the N-Terminal Domain (NTD) of the Spike Protein of SARS-CoV-2 Variants

Viruses, Journal Year: 2024, Volume and Issue: 16(12), P. 1836 - 1836

Published: Nov. 27, 2024

Most studies on the docking of ivermectin spike protein SARS-CoV-2 concern receptor binding domain (RBD) and, more precisely, RBD interface recognized by ACE2 receptor. The N-terminal (NTD), which controls initial attachment virus to lipid raft gangliosides, has not received attention it deserves. In this study, we combined molecular modeling and physicochemical approaches analyze mode interaction with NTD-facing rafts host cell membrane. We characterize a area that presents point mutations deletions in successive variants from strain omicron KP.3 circulating many countries 2024. show exceptional flexibility, allowing drug bind all tested. energy is specific each variant, classification according their affinity for following ascending order: Omicron < Delta BA.5 Alpha Wuhan (B.1) BA.1. site subject important variations NTD, including Y144 deletion. It overlaps ganglioside as demonstrated studies. These results suggest new mechanism antiviral action based competitive inhibition rafts. current variant still ivermectin, although an slightly lower than strain.

Language: Английский

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Changes in total charge on spike protein of SARS-CoV-2 in emerging lineages

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 23, 2023

Motivation: Charged amino acid residues on the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been shown to influence its binding different cell surface receptors, non-specific electrostatic interactions with environment, and structural stability conformation. It is therefore important obtain a good understanding mutations that affect total charge which arisen across SARS-CoV-2 lineages during course virus' evolution. Results: We analyse change in number ionizable acids corresponding proteins almost 2200 emerged over span pandemic. Our results show previously observed trend toward an increase positive variants concern has essentially stopped emergence early omicron variants. Furthermore, recently greater diversity terms their composition acids. also demonstrate patterns are characteristic related within broader clade division phylogenetic tree. Due ubiquity biological our findings relevant for broad range studies dealing environment. Availability: The data underlying article available online Supplementary Material.

Language: Английский

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