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

Autores
Mogro, Ezequiel Gerardo; Bottero, Daniela; Lozano, Mauricio Javier
Año de publicación
2022
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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
Materia
Biología
Codon usage bias
SARS-CoV-2
COVID-19
Betacoronavirus
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
SEDICI (UNLP)
Institución
Universidad Nacional de La Plata
OAI Identificador
oai:sedici.unlp.edu.ar:10915/159865
Acceder
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network_name_str SEDICI (UNLP)
spelling Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemicMogro, Ezequiel GerardoBottero, DanielaLozano, Mauricio JavierBiologíaCodon usage biasSARS-CoV-2COVID-19BetacoronavirusSARS-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 Molecular2022info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionArticulohttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://sedici.unlp.edu.ar/handle/10915/159865enginfo:eu-repo/semantics/altIdentifier/issn/1096-0341info:eu-repo/semantics/altIdentifier/doi/10.1016/j.virol.2022.01.011info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)reponame:SEDICI (UNLP)instname:Universidad Nacional de La Platainstacron:UNLP2025-10-22T17:22:43Zoai:sedici.unlp.edu.ar:10915/159865Institucionalhttp://sedici.unlp.edu.ar/Universidad públicaNo correspondehttp://sedici.unlp.edu.ar/oai/snrdalira@sedici.unlp.edu.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:13292025-10-22 17:22:44.183SEDICI (UNLP) - Universidad Nacional de La Platafalse
dc.title.none.fl_str_mv Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic
title Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic
spellingShingle Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic
Mogro, Ezequiel Gerardo
Biología
Codon usage bias
SARS-CoV-2
COVID-19
Betacoronavirus
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
dc.creator.none.fl_str_mv Mogro, Ezequiel Gerardo
Bottero, Daniela
Lozano, Mauricio Javier
author Mogro, Ezequiel Gerardo
author_facet Mogro, Ezequiel Gerardo
Bottero, Daniela
Lozano, Mauricio Javier
author_role author
author2 Bottero, Daniela
Lozano, Mauricio Javier
author2_role author
author
dc.subject.none.fl_str_mv Biología
Codon usage bias
SARS-CoV-2
COVID-19
Betacoronavirus
topic Biología
Codon usage bias
SARS-CoV-2
COVID-19
Betacoronavirus
dc.description.none.fl_txt_mv 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
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.
publishDate 2022
dc.date.none.fl_str_mv 2022
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
Articulo
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://sedici.unlp.edu.ar/handle/10915/159865
url http://sedici.unlp.edu.ar/handle/10915/159865
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/issn/1096-0341
info:eu-repo/semantics/altIdentifier/doi/10.1016/j.virol.2022.01.011
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:SEDICI (UNLP)
instname:Universidad Nacional de La Plata
instacron:UNLP
reponame_str SEDICI (UNLP)
collection SEDICI (UNLP)
instname_str Universidad Nacional de La Plata
instacron_str UNLP
institution UNLP
repository.name.fl_str_mv SEDICI (UNLP) - Universidad Nacional de La Plata
repository.mail.fl_str_mv alira@sedici.unlp.edu.ar
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