Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic

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 a...

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Autores principales: Mogro, Ezequiel Gerardo, Bottero, Daniela, Lozano, Mauricio Javier
Formato: Articulo
Lenguaje:Inglés
Publicado: 2022
Materias:
Biología
Codon usage bias
SARS-CoV-2
COVID-19
Betacoronavirus
Acceso en línea:http://sedici.unlp.edu.ar/handle/10915/159865
Aporte de:
SEDICI (UNLP) de Universidad Nacional de La Plata
id I19-R120-10915-159865
record_format dspace
spelling I19-R120-10915-1598652023-11-08T20:07:20Z http://sedici.unlp.edu.ar/handle/10915/159865 Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic Mogro, Ezequiel Gerardo Bottero, Daniela Lozano, Mauricio Javier 2022 2023-11-07T14:50:24Z en Biología Codon usage bias SARS-CoV-2 COVID-19 Betacoronavirus 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. Instituto de Biotecnología y Biología Molecular Articulo Articulo http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) application/pdf
institution Universidad Nacional de La Plata
institution_str I-19
repository_str R-120
collection SEDICI (UNLP)
language Inglés
topic Biología
Codon usage bias
SARS-CoV-2
COVID-19
Betacoronavirus
spellingShingle Biología
Codon usage bias
SARS-CoV-2
COVID-19
Betacoronavirus
Mogro, Ezequiel Gerardo
Bottero, Daniela
Lozano, Mauricio Javier
Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic
topic_facet Biología
Codon usage bias
SARS-CoV-2
COVID-19
Betacoronavirus
description 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.
format Articulo
Articulo
author Mogro, Ezequiel Gerardo
Bottero, Daniela
Lozano, Mauricio Javier
author_facet Mogro, Ezequiel Gerardo
Bottero, Daniela
Lozano, Mauricio Javier
author_sort Mogro, Ezequiel Gerardo
title Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic
title_short Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic
title_full Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic
title_fullStr Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic
title_full_unstemmed Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic
title_sort analysis of sars-cov-2 synonymous codon usage evolution throughout the covid-19 pandemic
publishDate 2022
url http://sedici.unlp.edu.ar/handle/10915/159865
work_keys_str_mv AT mogroezequielgerardo analysisofsarscov2synonymouscodonusageevolutionthroughoutthecovid19pandemic
AT botterodaniela analysisofsarscov2synonymouscodonusageevolutionthroughoutthecovid19pandemic
AT lozanomauriciojavier analysisofsarscov2synonymouscodonusageevolutionthroughoutthecovid19pandemic
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