Increased preference for lysine over arginine in spike proteins of SARS-CoV-2 BA.2.86 variant and its daughter lineages

PLoS ONE, Journal Year: 2025, Volume and Issue: 20(4), P. e0320891 - e0320891

Published: April 7, 2025

The COVID-19 pandemic offered an unprecedented glimpse into the evolution of its causative virus, SARS-CoV-2. It has been estimated that since outbreak in late 2019, virus explored all possible alternatives terms missense mutations for sites polypeptide chain. Spike protein exhibits largest sequence variation particular, with many individual impacting target recognition, cellular entry, and endosomal escape virus. Moreover, recent studies unveiled a significant increase total charge on spike during initial period pandemic. While this trend recently come to halt, we perform sequence-based analysis 2665 SARS-CoV-2 variants which shows ionizable amino acids continue occur newly emerging variants, notable differences between lineages from different clades. What is more, show within can acquire positive charge, prominent preference lysine residues over arginine residues. This lysine-to-arginine ratio increased at several points evolution, most BA.2.86 sublineages, including dominant JN.1, KP.3, XEC variants. consequence structural regions now among highest viral species Coronaviridae family. impact high proteins daughter fitness remains unclear; discuss potential mechanisms could play role serve as starting point further studies.

Language: Английский

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Genomic Insights into SARS-CoV-2 Evolution: Nucleocapsid Gene Mutations in West Sumatra, Indonesia

International Journal of Research and Review, Journal Year: 2024, Volume and Issue: 11(5), P. 607 - 613

Published: June 10, 2024

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic has necessitated a comprehensive understanding of viral mutations, particularly in the nucleocapsid protein, which plays crucial role virus's life cycle and interaction with host immune system. This study aims to analyze (N) gene mutations SARS-CoV-2 variants isolated from West Sumatra during pandemic. A dataset 352 sequences local COVID-19 cases was examined identify N assess their prevalence across different variants. primary identified were R203K G204R ancestral Omicron However, D63G D377Y mutation is present Delta variant. These are implicated enhancing infectivity potential evasion. Notably, variant showed additional deletions (P13L, E31-, R32-, S33-, S413R) that harm protein expansion for structural stability functionality protein. conservation specific suggests fundamental replication interaction. Variant-specific may represent adaptive responses pressure or other environmental factors, significant implications transmissibility pathogenicity. Understanding impact provides critical insights into evolutionary dynamics aids developing effective vaccines therapeutics. Continued surveillance detailed functional studies essential manage prepare future outbreaks. Keywords: SARS-CoV-2, gene, evolution.

Language: Английский

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Genome Characterization and Phylogenetic Analysis of Scale Drop Disease Virus Isolated from Asian Seabass (Lates calcarifer)

Animals, Journal Year: 2024, Volume and Issue: 14(14), P. 2097 - 2097

Published: July 18, 2024

Scale drop disease virus (SDDV), a double-stranded DNA in the family

Language: Английский

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Computational Analysis of the accumulation of mutations in therapeutically important RNA viral proteins during pandemics with special emphasis on SARS-CoV-2

Journal of Molecular Biology, Journal Year: 2024, Volume and Issue: 436(19), P. 168716 - 168716

Published: July 22, 2024

Language: Английский

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Leveraging neural networks to correct FoldX free energy estimates

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 25, 2024

Proteins play a pivotal role in many biological processes, and changes their amino acid sequences can lead to dysfunction disease. These affect protein folding or interaction with other biomolecules, such as preventing antibodies from inhibiting viral infection causing proteins misfold. The ability predict the effects of mutations is crucial. Although experimental techniques accurately quantify effect on free energies protein-protein binding energies, they are often time-consuming costly. By contrast, computational offer fast cost-effective alternatives for estimating but typically suffer lower accuracy. Enhancing accuracy predictions therefore high importance, potential greatly impact fields ranging drug design understanding disease mechanisms. One widely used method, FoldX, capable rapidly predicting relative stability (ΔΔG

Language: Английский

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Tracking cryptic SARS-CoV-2 hospital outbreak through quasispecies analysis

Virology Journal, Journal Year: 2024, Volume and Issue: 21(1)

Published: Dec. 21, 2024

Language: Английский

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