Betacoronaviruses genome analysis reveals evolution toward specific codons usage: Implications for SARS‐CoV‐2 mitigation strategies

Detalhes bibliográficos
Autor(a) principal: Lopes, Elisson N.
Data de Publicação: 2020
Outros Autores: Fonseca, Vagner, Frias, Diego, Tosta, Stephane, Salgado, Àlvaro, Vialle, Ricardo Assunção, Eduardo, Toscano S. Paulo, Barreto, Fernanda K., Azevedo, Vasco Ariston de, Guarino, Michele, Angeletti, Sílvia, Ciccozzi, Massimo, Alcantara, Luiz C. Junior, Giovanetti, Marta
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/49070
Resumo: Universidade Federal de Minas Gerais. Instituto de Ciencias Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil.
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spelling Lopes, Elisson N.Fonseca, VagnerFrias, DiegoTosta, StephaneSalgado, ÀlvaroVialle, Ricardo AssunçãoEduardo, Toscano S. PauloBarreto, Fernanda K.Azevedo, Vasco Ariston deGuarino, MicheleAngeletti, SílviaCiccozzi, MassimoAlcantara, Luiz C. JuniorGiovanetti, Marta2021-09-14T10:52:26Z2021-09-14T10:52:26Z2020LOPES, Elisson N. et al. Betacoronaviruses genome analysis reveals evolution toward specific codons usage: Implications for SARS‐CoV‐2 mitigation strategies. Journal of Medical Virology, p.1-5, 2021.1096-9071https://www.arca.fiocruz.br/handle/icict/4907010.1002/jmv.27056engWileySARS-CoV-2COVID-19Deotimização do códonUso de codonCoronavírusCodon deoptimizationCodon usageCoronavirusesCOVID-19SARS-CoV-2Betacoronaviruses genome analysis reveals evolution toward specific codons usage: Implications for SARS‐CoV‐2 mitigation strategiesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleUniversidade Federal de Minas Gerais. Instituto de Ciencias Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil.KwaZulu‐Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZuluNatal, Durban, South Africa / Ministério da Saúde. Secretaria de Vigilância em Saúde. Coordenação Geral dos Laboratórios de Saúde Pública. Brasília, DF, Brasil.Universidade do Estado da Bahia. Departamento de Ciências Exatas e da Terra. Salvador, BA, Brasil.Universidade Federal de Minas Gerais. Instituto de Ciencias Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil.Universidade Federal de Minas Gerais. Instituto de Ciencias Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil.Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.Universidade Federal do Rio Grande do Norte. Departamento de Bioquímica. Laboratório de Biologia Molecular Aplicada. Natal RN, Brasil.Universidade Federal da Bahia. Vitória da Conquista, BA, Brasil.Universidade Federal de Minas Gerais. Instituto de Ciencias Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil.Department of Gastrointestinal Diseases, Campus Bio‐Medico University. Rome, Italy.Unit of Clinical Laboratory Science, University Campus Bio‐Medico of Rome. Rome, Italy.Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus. Rome, Italy.Universidade Federal de Minas Gerais. Instituto de Ciencias Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brasil.Universidade Federal de Minas Gerais. Instituto de Ciencias Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brasil.Abstract Since the start of the coronavirus disease 2019 (COVID‐19) pandemic, the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has rapidly widespread worldwide becoming one of the major global public health issues of the last centuries. Currently, COVID‐19 vaccine rollouts are finally upon us carrying the hope of herd immunity once a sufficient proportion of the population has been vaccinated or infected, as a new horizon. However, the emergence of SARS‐CoV‐2 variants brought concerns since, as the virus is exposed to environmental selection pressures, it can mutate and evolve, generating variants that may possess enhanced virulence. Codon usage analysis is a strategy to elucidate the evolutionary pressure of the viral genome suffered by different hosts, as possible cause of the emergence of new variants. Therefore, to get a better picture of the SARS‐CoV‐2 codon bias, we first identified the relative codon usage rate of all Betacoronaviruses lineages. Subsequently, we correlated putative cognate transfer ribo nucleic acid (tRNAs) to reveal how those viruses adapt to hosts in relation to their preferred codon usage. Our analysis revealed seven preferred codons located in three different open reading frame which appear preferentially used by SARS‐CoV‐2. In ad dition, the tRNA adaptation analysis indicates a wide strategy of competition between the virus and mammalian as principal hosts highlighting the importance to reinforce the genomic monitoring to prompt identify any potential adaptation of the virus into new potential hosts which appear to be crucial to prevent and mitigate the pandemic.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; 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dc.title.pt_BR.fl_str_mv Betacoronaviruses genome analysis reveals evolution toward specific codons usage: Implications for SARS‐CoV‐2 mitigation strategies
title Betacoronaviruses genome analysis reveals evolution toward specific codons usage: Implications for SARS‐CoV‐2 mitigation strategies
spellingShingle Betacoronaviruses genome analysis reveals evolution toward specific codons usage: Implications for SARS‐CoV‐2 mitigation strategies
Lopes, Elisson N.
SARS-CoV-2
COVID-19
Deotimização do códon
Uso de codon
Coronavírus
Codon deoptimization
Codon usage
Coronaviruses
COVID-19
SARS-CoV-2
title_short Betacoronaviruses genome analysis reveals evolution toward specific codons usage: Implications for SARS‐CoV‐2 mitigation strategies
title_full Betacoronaviruses genome analysis reveals evolution toward specific codons usage: Implications for SARS‐CoV‐2 mitigation strategies
title_fullStr Betacoronaviruses genome analysis reveals evolution toward specific codons usage: Implications for SARS‐CoV‐2 mitigation strategies
title_full_unstemmed Betacoronaviruses genome analysis reveals evolution toward specific codons usage: Implications for SARS‐CoV‐2 mitigation strategies
title_sort Betacoronaviruses genome analysis reveals evolution toward specific codons usage: Implications for SARS‐CoV‐2 mitigation strategies
author Lopes, Elisson N.
author_facet Lopes, Elisson N.
Fonseca, Vagner
Frias, Diego
Tosta, Stephane
Salgado, Àlvaro
Vialle, Ricardo Assunção
Eduardo, Toscano S. Paulo
Barreto, Fernanda K.
Azevedo, Vasco Ariston de
Guarino, Michele
Angeletti, Sílvia
Ciccozzi, Massimo
Alcantara, Luiz C. Junior
Giovanetti, Marta
author_role author
author2 Fonseca, Vagner
Frias, Diego
Tosta, Stephane
Salgado, Àlvaro
Vialle, Ricardo Assunção
Eduardo, Toscano S. Paulo
Barreto, Fernanda K.
Azevedo, Vasco Ariston de
Guarino, Michele
Angeletti, Sílvia
Ciccozzi, Massimo
Alcantara, Luiz C. Junior
Giovanetti, Marta
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Lopes, Elisson N.
Fonseca, Vagner
Frias, Diego
Tosta, Stephane
Salgado, Àlvaro
Vialle, Ricardo Assunção
Eduardo, Toscano S. Paulo
Barreto, Fernanda K.
Azevedo, Vasco Ariston de
Guarino, Michele
Angeletti, Sílvia
Ciccozzi, Massimo
Alcantara, Luiz C. Junior
Giovanetti, Marta
dc.subject.other.pt_BR.fl_str_mv SARS-CoV-2
COVID-19
Deotimização do códon
Uso de codon
Coronavírus
topic SARS-CoV-2
COVID-19
Deotimização do códon
Uso de codon
Coronavírus
Codon deoptimization
Codon usage
Coronaviruses
COVID-19
SARS-CoV-2
dc.subject.en.pt_BR.fl_str_mv Codon deoptimization
Codon usage
Coronaviruses
COVID-19
SARS-CoV-2
description Universidade Federal de Minas Gerais. Instituto de Ciencias Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil.
publishDate 2020
dc.date.issued.fl_str_mv 2020
dc.date.accessioned.fl_str_mv 2021-09-14T10:52:26Z
dc.date.available.fl_str_mv 2021-09-14T10:52:26Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv LOPES, Elisson N. et al. Betacoronaviruses genome analysis reveals evolution toward specific codons usage: Implications for SARS‐CoV‐2 mitigation strategies. Journal of Medical Virology, p.1-5, 2021.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/49070
dc.identifier.issn.pt_BR.fl_str_mv 1096-9071
dc.identifier.doi.none.fl_str_mv 10.1002/jmv.27056
identifier_str_mv LOPES, Elisson N. et al. Betacoronaviruses genome analysis reveals evolution toward specific codons usage: Implications for SARS‐CoV‐2 mitigation strategies. Journal of Medical Virology, p.1-5, 2021.
1096-9071
10.1002/jmv.27056
url https://www.arca.fiocruz.br/handle/icict/49070
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Wiley
publisher.none.fl_str_mv Wiley
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
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