An entropy-based study on the mutational landscape of SARS-CoV-2 in USA: Comparing different variants and revealing co-mutational behavior of proteins DOI Creative Commons
Daniele Santoni

Gene, Journal Year: 2024, Volume and Issue: 922, P. 148556 - 148556

Published: May 14, 2024

COVID-19 emergency has pushed the international scientific community to use every resource combat spread of virus, understand its biology and predict possible evolution in terms new variants. Since first SARS-CoV-2 virus nucleotide amino acid sequences were made available, information theory was used study how viral content changing over time then trace mutational landscape. In this work we analyzed collected mainly USA a period from March 2020 until December 2022 computed mutation profiles proteins through an entropy-based approach using Shannon Entropy Hellinger distance. This representation allows at-a-glance view landscape can provide insights on different points view. Non-structural typically showed flat profiles, characterized by very low Average Entropy, while accessory structural mostly non uniform high often coupled with predominance Interestingly NSP2 protein, whose function is currently still debated, falls same branch NSP14 NSP10 phylogenetic tree mutations constructed correlations suggesting co-evolution those functional link each other. To best our knowledge based massive amount data (n=107,939,973) that analyzes entropy point depicts temporal profile protein virus.

Language: Английский

Early mutational signatures and transmissibility of SARS-CoV-2 Gamma and Lambda variants in Chile DOI Creative Commons
Karen Oróstica, Sebastian Mohr, Jonas Dehning

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: July 11, 2024

Abstract Genomic surveillance (GS) programmes were crucial in identifying and quantifying the mutating patterns of SARS-CoV-2 during COVID-19 pandemic. In this work, we develop a Bayesian framework to quantify relative transmissibility different variants tailored for regions with limited GS. We use it study Chile. Among 3443 genomes collected between January June 2021, where sampling was designed be representative, Gamma (P.1), Lambda (C.37), Alpha (B.1.1.7), B.1.1.348, B.1.1 lineages predominant. found that variants’ reproduction numbers 5% (95% CI: [1%, 14%]) 16% [11%, 21%]) larger than Alpha’s, respectively. Besides, observed systematic mutation enrichment Spike gene all circulating variants, which strongly correlated studied period (r = 0.93, p-value 0.025). also characterised mutational signatures local samples their evolution over time progress vaccination, comparing them those other worldwide. Altogether, our work provides reliable method variant under subsampling emphasises importance continuous genomic surveillance.

Language: Английский

Citations

7
SARS-CoV-2 biological clones are genetically heterogeneous and include clade-discordant residues DOI Creative Commons
Ana Isabel de Ávila, María Eugenia Soria, Brenda Martínez‐González

et al.

Journal of Virology, Journal Year: 2025, Volume and Issue: unknown

Published: April 24, 2025

ABSTRACT Defective genomes are part of SARS-CoV-2 quasispecies. High-resolution, ultra-deep sequencing bulk RNA from viral populations does not distinguish mutations, insertions, and deletions in viable those defective genomes. To quantify infectious variant progeny, virus four individual plaques (biological clones) a preparation isolate USA-WA1/2020, formed on Vero E6 cell monolayers, was subjected to further biological cloning yield 9 second-generation 15 third-generation sub-clones. Consensus genomic sequences the clones sub-clones included an average 2.8 variations per genome, relative consensus sequence parental USA-WA1/2020 virus. This value is 6.5-fold lower than estimates for other viruses such as bacteriophage Qβ, foot-and-mouth disease virus, or hepatitis C culture. The mutant spectrum complexity nsp12 (polymerase)- spike (S)-coding region unique progeny each 10 sub-clones; they shared 2.4% total 164 different mutations scored 3,719 residues that were screened. presence minority out-of-frame revealed ease genome production genome. Several low-frequency point clade-discordant typical but served define future clades. Implications adaptability COVID-19 control heterogeneity generation complex spectra discussed. IMPORTANCE Sequencing means identify located distinction particularly important populations, SARS-CoV-2, contain large proportions By sub-clones, we quantified complement be exhibited by viruses. difference may due reduced mutation rate limited tolerance coronavirus incorporate remain functional combination both influences. suggests limitations occupation space SARS-CoV-2. However, rapidly generated suggest aptness confront selective constraints.

Language: Английский

Citations

0
An entropy-based study on the mutational landscape of SARS-CoV-2 in USA: Comparing different variants and revealing co-mutational behavior of proteins DOI Creative Commons
Daniele Santoni

Gene, Journal Year: 2024, Volume and Issue: 922, P. 148556 - 148556

Published: May 14, 2024

COVID-19 emergency has pushed the international scientific community to use every resource combat spread of virus, understand its biology and predict possible evolution in terms new variants. Since first SARS-CoV-2 virus nucleotide amino acid sequences were made available, information theory was used study how viral content changing over time then trace mutational landscape. In this work we analyzed collected mainly USA a period from March 2020 until December 2022 computed mutation profiles proteins through an entropy-based approach using Shannon Entropy Hellinger distance. This representation allows at-a-glance view landscape can provide insights on different points view. Non-structural typically showed flat profiles, characterized by very low Average Entropy, while accessory structural mostly non uniform high often coupled with predominance Interestingly NSP2 protein, whose function is currently still debated, falls same branch NSP14 NSP10 phylogenetic tree mutations constructed correlations suggesting co-evolution those functional link each other. To best our knowledge based massive amount data (n=107,939,973) that analyzes entropy point depicts temporal profile protein virus.

Language: Английский

Citations

2