Codon Usage Bias in Human RNA Viruses and Its Impact on Viral Translation, Fitness, and Evolution

Synonymous codon usage (codon bias) greatly influences not only translation but also mRNA stability. In vertebrates, highly expressed genes preferentially use codons with an optimal tRNA adaptation index (tAI) that mostly end in C or G. Surprisingly, the codon usage of viruses infecting humans often...

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Detalles Bibliográficos
Autor: Ventoso, Iván
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2025
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/401622
Acceso en línea:http://hdl.handle.net/10261/401622
Access Level:acceso abierto
Palabra clave:Human RNA virus
Codon usage bias
Synonymous codons
tRNAs
Translation
Virus fitness
Virus evolution
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spelling Codon Usage Bias in Human RNA Viruses and Its Impact on Viral Translation, Fitness, and EvolutionVentoso, IvánHuman RNA virusCodon usage biasSynonymous codonstRNAsTranslationVirus fitnessVirus evolutionSynonymous codon usage (codon bias) greatly influences not only translation but also mRNA stability. In vertebrates, highly expressed genes preferentially use codons with an optimal tRNA adaptation index (tAI) that mostly end in C or G. Surprisingly, the codon usage of viruses infecting humans often deviates from optimality, showing an enrichment in A/U-ending codons, which are generally associated with slow decoding and reduced mRNA stability. This observation is particularly evident in RNA viruses causing respiratory illnesses in humans. This review analyzes the mutational and selective forces that shape nucleotide composition and codon usage drift in human RNA viruses, as well as their impact on translation, viral fitness, and evolution. It also describes how some viruses overcome suboptimal codon usage to outcompete host mRNA for translation. Finally, the roles of viral tropism and host adaptation in codon usage bias of prototypical viruses are discussed.This work was supported by a grant from the Spanish Ministry of Science and Innovation (PID2021-125844OB-I00).Peer reviewedMultidisciplinary Digital Publishing InstituteMinisterio de Ciencia e Innovación (España)Agencia Estatal de Investigación (España)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2025202520252025info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/401622reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-125844OB-I00The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.3390/v17091218https://doi.org/10.3390/v17091218Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/4016222026-05-22T06:33:51Z
dc.title.none.fl_str_mv Codon Usage Bias in Human RNA Viruses and Its Impact on Viral Translation, Fitness, and Evolution
title Codon Usage Bias in Human RNA Viruses and Its Impact on Viral Translation, Fitness, and Evolution
spellingShingle Codon Usage Bias in Human RNA Viruses and Its Impact on Viral Translation, Fitness, and Evolution
Ventoso, Iván
Human RNA virus
Codon usage bias
Synonymous codons
tRNAs
Translation
Virus fitness
Virus evolution
title_short Codon Usage Bias in Human RNA Viruses and Its Impact on Viral Translation, Fitness, and Evolution
title_full Codon Usage Bias in Human RNA Viruses and Its Impact on Viral Translation, Fitness, and Evolution
title_fullStr Codon Usage Bias in Human RNA Viruses and Its Impact on Viral Translation, Fitness, and Evolution
title_full_unstemmed Codon Usage Bias in Human RNA Viruses and Its Impact on Viral Translation, Fitness, and Evolution
title_sort Codon Usage Bias in Human RNA Viruses and Its Impact on Viral Translation, Fitness, and Evolution
dc.creator.none.fl_str_mv Ventoso, Iván
author Ventoso, Iván
author_facet Ventoso, Iván
author_role author
dc.contributor.none.fl_str_mv Ministerio de Ciencia e Innovación (España)
Agencia Estatal de Investigación (España)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Human RNA virus
Codon usage bias
Synonymous codons
tRNAs
Translation
Virus fitness
Virus evolution
topic Human RNA virus
Codon usage bias
Synonymous codons
tRNAs
Translation
Virus fitness
Virus evolution
description Synonymous codon usage (codon bias) greatly influences not only translation but also mRNA stability. In vertebrates, highly expressed genes preferentially use codons with an optimal tRNA adaptation index (tAI) that mostly end in C or G. Surprisingly, the codon usage of viruses infecting humans often deviates from optimality, showing an enrichment in A/U-ending codons, which are generally associated with slow decoding and reduced mRNA stability. This observation is particularly evident in RNA viruses causing respiratory illnesses in humans. This review analyzes the mutational and selective forces that shape nucleotide composition and codon usage drift in human RNA viruses, as well as their impact on translation, viral fitness, and evolution. It also describes how some viruses overcome suboptimal codon usage to outcompete host mRNA for translation. Finally, the roles of viral tropism and host adaptation in codon usage bias of prototypical viruses are discussed.
publishDate 2025
dc.date.none.fl_str_mv 2025
2025
2025
2025
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/401622
url http://hdl.handle.net/10261/401622
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-125844OB-I00
The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.3390/v17091218
https://doi.org/10.3390/v17091218
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
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