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Updated: Oct 4, 2025

Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples
Published on: June 30, 2023
Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic
Ezequiel G Mogro1, Daniela Bottero1, Mauricio J Lozano1
1Instituto de Biotecnología y Biología Molecular (IBBM), CONICET, CCT-La Plata, Universidad Nacional de La Plata (UNLP), Argentina.
Abstract:
SARS-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 evolution 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.
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