A comprehensive analysis of genome composition and codon usage patterns of emerging coronaviruses
Resumen:
An outbreak of atypical pneumonia caused by a novel Betacoronavirus (βCoV), named SARS-CoV-2 has been declared a public health emergency of international concern by the World Health Organization. In order to gain insight into the emergence, evolution and adaptation of SARS-CoV-2 viruses, a comprehensive analysis of genome composition and codon usage of βCoV circulating in China was performed. A biased nucleotide composition was found for SARS-CoV-2 genome. This bias in genomic composition is reflected in its codon and amino acid usage patterns. The overall codon usage in SARS-CoV-2 is similar among themselves and slightly biased. Most of the highly frequent codons are A- and U-ending, which strongly suggests that mutational bias is the main force shaping codon usage in this virus. Significant differences in relative synonymous codon usage frequencies among SARS-CoV-2 and human cells were found. These differences are due to codon usage preferences.
| 2020 | |
| ANII; CSIC | |
|
Coronavirus Evolution Codon usage Wuhan 2019-nCoV SARS-CoV-2 |
|
| Inglés | |
| Universidad de la República | |
| COLIBRI | |
| https://hdl.handle.net/20.500.12008/31694 | |
| Acceso abierto | |
| Licencia Creative Commons Atribución - No Comercial - Sin Derivadas (CC - By-NC-ND 4.0) |
| _version_ | 1807522790155223040 |
|---|---|
| author | López Tort, Luis Fernando |
| author2 | Castells Bauer, Matías Cristina, Juan |
| author2_role | author author |
| author_facet | López Tort, Luis Fernando Castells Bauer, Matías Cristina, Juan |
| author_role | author |
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| collection | COLIBRI |
| dc.contributor.filiacion.none.fl_str_mv | López Tort Luis Fernando, Universidad de la República (Uruguay). CENUR Castells Bauer Matías, Universidad de la República (Uruguay). CENUR Cristina Juan, Universidad de la República (Uruguay). Facultad de Ciencias. Centro de Investigaciones Nucleares. |
| dc.creator.none.fl_str_mv | López Tort, Luis Fernando Castells Bauer, Matías Cristina, Juan |
| dc.date.accessioned.none.fl_str_mv | 2022-05-30T14:36:21Z |
| dc.date.available.none.fl_str_mv | 2022-05-30T14:36:21Z |
| dc.date.issued.none.fl_str_mv | 2020 |
| dc.description.abstract.none.fl_txt_mv | An outbreak of atypical pneumonia caused by a novel Betacoronavirus (βCoV), named SARS-CoV-2 has been declared a public health emergency of international concern by the World Health Organization. In order to gain insight into the emergence, evolution and adaptation of SARS-CoV-2 viruses, a comprehensive analysis of genome composition and codon usage of βCoV circulating in China was performed. A biased nucleotide composition was found for SARS-CoV-2 genome. This bias in genomic composition is reflected in its codon and amino acid usage patterns. The overall codon usage in SARS-CoV-2 is similar among themselves and slightly biased. Most of the highly frequent codons are A- and U-ending, which strongly suggests that mutational bias is the main force shaping codon usage in this virus. Significant differences in relative synonymous codon usage frequencies among SARS-CoV-2 and human cells were found. These differences are due to codon usage preferences. |
| dc.description.sponsorship.none.fl_txt_mv | ANII; CSIC |
| dc.format.extent.es.fl_str_mv | 7 h. |
| dc.format.mimetype.es.fl_str_mv | application/pdf |
| dc.identifier.citation.es.fl_str_mv | López Tort, L, Castells Bauer, M y Cristina, J. "A comprehensive analysis of genome composition and codon usage patterns of emerging coronaviruses". Virus Research. [en línea] 2020, 283: 197976. 7 h. DOI: 10.1016/j.virusres.2020.197976 |
| dc.identifier.doi.none.fl_str_mv | 10.1016/j.virusres.2020.197976 |
| dc.identifier.issn.none.fl_str_mv | 0168-1702 |
| dc.identifier.uri.none.fl_str_mv | https://hdl.handle.net/20.500.12008/31694 |
| dc.language.iso.none.fl_str_mv | en eng |
| dc.publisher.es.fl_str_mv | Elsevier |
| dc.relation.ispartof.es.fl_str_mv | Virus Research, 2020, 283: 197976 |
| dc.rights.license.none.fl_str_mv | Licencia Creative Commons Atribución - No Comercial - Sin Derivadas (CC - By-NC-ND 4.0) |
| dc.rights.none.fl_str_mv | info:eu-repo/semantics/openAccess |
| dc.source.none.fl_str_mv | reponame:COLIBRI instname:Universidad de la República instacron:Universidad de la República |
| dc.subject.es.fl_str_mv | Coronavirus Evolution Codon usage Wuhan 2019-nCoV SARS-CoV-2 |
| dc.title.none.fl_str_mv | A comprehensive analysis of genome composition and codon usage patterns of emerging coronaviruses |
| dc.type.es.fl_str_mv | Artículo |
| dc.type.none.fl_str_mv | info:eu-repo/semantics/article |
| dc.type.version.none.fl_str_mv | info:eu-repo/semantics/publishedVersion |
| description | An outbreak of atypical pneumonia caused by a novel Betacoronavirus (βCoV), named SARS-CoV-2 has been declared a public health emergency of international concern by the World Health Organization. In order to gain insight into the emergence, evolution and adaptation of SARS-CoV-2 viruses, a comprehensive analysis of genome composition and codon usage of βCoV circulating in China was performed. A biased nucleotide composition was found for SARS-CoV-2 genome. This bias in genomic composition is reflected in its codon and amino acid usage patterns. The overall codon usage in SARS-CoV-2 is similar among themselves and slightly biased. Most of the highly frequent codons are A- and U-ending, which strongly suggests that mutational bias is the main force shaping codon usage in this virus. Significant differences in relative synonymous codon usage frequencies among SARS-CoV-2 and human cells were found. These differences are due to codon usage preferences. |
| eu_rights_str_mv | openAccess |
| format | article |
| id | COLIBRI_153cbb6739bc1b5fc17778fa56bbb6d0 |
| identifier_str_mv | López Tort, L, Castells Bauer, M y Cristina, J. "A comprehensive analysis of genome composition and codon usage patterns of emerging coronaviruses". Virus Research. [en línea] 2020, 283: 197976. 7 h. DOI: 10.1016/j.virusres.2020.197976 0168-1702 10.1016/j.virusres.2020.197976 |
| instacron_str | Universidad de la República |
| institution | Universidad de la República |
| instname_str | Universidad de la República |
| language | eng |
| language_invalid_str_mv | en |
| network_acronym_str | COLIBRI |
| network_name_str | COLIBRI |
| oai_identifier_str | oai:colibri.udelar.edu.uy:20.500.12008/31694 |
| publishDate | 2020 |
| reponame_str | COLIBRI |
| repository.mail.fl_str_mv | mabel.seroubian@seciu.edu.uy |
| repository.name.fl_str_mv | COLIBRI - Universidad de la República |
| repository_id_str | 4771 |
| rights_invalid_str_mv | Licencia Creative Commons Atribución - No Comercial - Sin Derivadas (CC - By-NC-ND 4.0) |
| spelling | López Tort Luis Fernando, Universidad de la República (Uruguay). CENURCastells Bauer Matías, Universidad de la República (Uruguay). CENURCristina Juan, Universidad de la República (Uruguay). Facultad de Ciencias. Centro de Investigaciones Nucleares.2022-05-30T14:36:21Z2022-05-30T14:36:21Z2020López Tort, L, Castells Bauer, M y Cristina, J. "A comprehensive analysis of genome composition and codon usage patterns of emerging coronaviruses". Virus Research. [en línea] 2020, 283: 197976. 7 h. DOI: 10.1016/j.virusres.2020.1979760168-1702https://hdl.handle.net/20.500.12008/3169410.1016/j.virusres.2020.197976An outbreak of atypical pneumonia caused by a novel Betacoronavirus (βCoV), named SARS-CoV-2 has been declared a public health emergency of international concern by the World Health Organization. In order to gain insight into the emergence, evolution and adaptation of SARS-CoV-2 viruses, a comprehensive analysis of genome composition and codon usage of βCoV circulating in China was performed. A biased nucleotide composition was found for SARS-CoV-2 genome. This bias in genomic composition is reflected in its codon and amino acid usage patterns. The overall codon usage in SARS-CoV-2 is similar among themselves and slightly biased. Most of the highly frequent codons are A- and U-ending, which strongly suggests that mutational bias is the main force shaping codon usage in this virus. Significant differences in relative synonymous codon usage frequencies among SARS-CoV-2 and human cells were found. 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Universidadhttps://udelar.edu.uy/https://www.colibri.udelar.edu.uy/oai/requestmabel.seroubian@seciu.edu.uyUruguayopendoar:47712024-07-25T14:28:39.106898COLIBRI 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| spellingShingle | A comprehensive analysis of genome composition and codon usage patterns of emerging coronaviruses López Tort, Luis Fernando Coronavirus Evolution Codon usage Wuhan 2019-nCoV SARS-CoV-2 |
| status_str | publishedVersion |
| title | A comprehensive analysis of genome composition and codon usage patterns of emerging coronaviruses |
| title_full | A comprehensive analysis of genome composition and codon usage patterns of emerging coronaviruses |
| title_fullStr | A comprehensive analysis of genome composition and codon usage patterns of emerging coronaviruses |
| title_full_unstemmed | A comprehensive analysis of genome composition and codon usage patterns of emerging coronaviruses |
| title_short | A comprehensive analysis of genome composition and codon usage patterns of emerging coronaviruses |
| title_sort | A comprehensive analysis of genome composition and codon usage patterns of emerging coronaviruses |
| topic | Coronavirus Evolution Codon usage Wuhan 2019-nCoV SARS-CoV-2 |
| url | https://hdl.handle.net/20.500.12008/31694 |
