Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic
Copyright policy )Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic
AbstractSARS-CoV-2, the seventh coronavirus known to infect humans, can cause severe life-threatening respiratory pathologies. To better understand SARS-CoV-2 evolution, genome-wide analyses have been made, including the general characterization of its codons usage profile. Here we present a bioinformatic analysis of the evo-lution of SARS-CoV-2 codon usage over time using complete genomes collected since December 2019. Our results show that SARS-CoV-2 codon usage pattern is antagonistic to, and it is getting farther away from that of the human host. Further, a selection of deoptimized codons over time, which was accompanied by a decrease in both the codon adaptation index and the effective number of codons, was observed. All together, these findings suggest that SARS-CoV-2 could be evolving, at least from the perspective of the synonymous codon usage, to become less pathogenic.Graphical Abstract
- National Scientific and Technical Research Council Argentina
- Instituto de Biotecnología y Biología Molecular Argentina
- National University of La Plata Argentina
Gene Expression Regulation, Viral, Artificial intelligence, Biología, Evolutionary biology, Genome, Viral, Infectious disease (medical specialty), Gene, Article, Evolution, Molecular, Computational biology, Betacoronavirus, Open Reading Frames, Selection (genetic algorithm), Biochemistry, Genetics and Molecular Biology, Genetics, Pathology, Humans, Disease, RNA Sequencing Data Analysis, Codon, Ribosome Structure and Translation Mechanisms, Codon Usage, Pandemics, Molecular Biology, Biology, Phylogeny, Genome, Pandemic, Adaptation (eye), SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), COVID-19, Life Sciences, Genomics, Computer science, Coronavirus disease 2019 (COVID-19), Organ Specificity, RNA Methylation and Modification in Gene Expression, FOS: Biological sciences, Medicine, Codon usage bias, Neuroscience
Gene Expression Regulation, Viral, Artificial intelligence, Biología, Evolutionary biology, Genome, Viral, Infectious disease (medical specialty), Gene, Article, Evolution, Molecular, Computational biology, Betacoronavirus, Open Reading Frames, Selection (genetic algorithm), Biochemistry, Genetics and Molecular Biology, Genetics, Pathology, Humans, Disease, RNA Sequencing Data Analysis, Codon, Ribosome Structure and Translation Mechanisms, Codon Usage, Pandemics, Molecular Biology, Biology, Phylogeny, Genome, Pandemic, Adaptation (eye), SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), COVID-19, Life Sciences, Genomics, Computer science, Coronavirus disease 2019 (COVID-19), Organ Specificity, RNA Methylation and Modification in Gene Expression, FOS: Biological sciences, Medicine, Codon usage bias, Neuroscience
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