tetano
Editor, Senior Moderator
Virology
. 2022 Feb 2;568:56-71.
doi: 10.1016/j.virol.2022.01.011. Online ahead of print.
Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic
Ezequiel G Mogro[SUP] 1 [/SUP], Daniela Bottero[SUP] 1 [/SUP], Mauricio J Lozano[SUP] 2 [/SUP]
Affiliations
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.
Keywords: Betacoronavirus; COVID-19; Codon usage bias; SARS-CoV-2.
. 2022 Feb 2;568:56-71.
doi: 10.1016/j.virol.2022.01.011. Online ahead of print.
Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic
Ezequiel G Mogro[SUP] 1 [/SUP], Daniela Bottero[SUP] 1 [/SUP], Mauricio J Lozano[SUP] 2 [/SUP]
Affiliations
- PMID: 35134624
- PMCID: PMC8808327
- DOI: 10.1016/j.virol.2022.01.011
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.
Keywords: Betacoronavirus; COVID-19; Codon usage bias; SARS-CoV-2.