Phylogenetic analysis of SARS‐CoV‐2 in the first few months since its emergence

Autores
Pereson, Matías J.; Mojsiejczuk, Laura Noelia; Martínez, Alfredo P.; Flichman, Diego Martin; García, Gabriel Hugo; Di Lello, Federico Alejandro
Año de publicación
2020
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
During the first months of SARS‐CoV‐2 evolution in a new host, contrasting hypotheses have been proposed about the way the virus has evolved and diversified worldwide. The aim of this study was to perform a comprehensive evolutionary analysis to describe the human outbreak and the evolutionary rate of different genomic regions of SARS‐CoV‐2.The molecular evolution in nine genomic regions of SARS‐CoV‐2 was analyzed using three different approaches: phylogenetic signal assessment, emergence of amino acid substitutions, and Bayesian evolutionary rate estimation in eight successive fortnights since the virus emergence.All observed phylogenetic signals were very low and tree topologies were in agreement with those signals. However, after four months of evolution, it was possible to identify regions revealing an incipient viral lineage formation despite the low phylogenetic signal, since fortnight 3. Finally, the SARS‐CoV‐2 evolutionary rate for regions nsp3 and S, the ones presenting greater variability, was estimated as 1.37 x 10‐3 and 2.19 x 10‐3 substitution/site/year, respectively.In conclusion, results from this work about the variable diversity of crucial viral regions and determination of the evolutionary rate are consequently decisive to understand essential features of viral emergence. In turn, findings may allow the first time characterization of the evolutionary rate of S protein, crucial for vaccine development.
Fil: Pereson, Matías J.. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Virología; Argentina
Fil: Mojsiejczuk, Laura Noelia. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay; Argentina
Fil: Martínez, Alfredo P.. Centro de Educaciones Médicas e Investigación Clínica "Norberto Quirno"; Argentina
Fil: Flichman, Diego Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas en Retrovirus y Sida. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas en Retrovirus y Sida; Argentina
Fil: García, Gabriel Hugo. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Virología; Argentina
Fil: Di Lello, Federico Alejandro. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay; Argentina
Materia
SARS-COV-2
PHYLOGENY
EVOLUTION
EVOLUTIONARY RATE
COVID-19
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/115890
Acceder
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network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Phylogenetic analysis of SARS‐CoV‐2 in the first few months since its emergencePereson, Matías J.Mojsiejczuk, Laura NoeliaMartínez, Alfredo P.Flichman, Diego MartinGarcía, Gabriel HugoDi Lello, Federico AlejandroSARS-COV-2PHYLOGENYEVOLUTIONEVOLUTIONARY RATECOVID-19https://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1During the first months of SARS‐CoV‐2 evolution in a new host, contrasting hypotheses have been proposed about the way the virus has evolved and diversified worldwide. The aim of this study was to perform a comprehensive evolutionary analysis to describe the human outbreak and the evolutionary rate of different genomic regions of SARS‐CoV‐2.The molecular evolution in nine genomic regions of SARS‐CoV‐2 was analyzed using three different approaches: phylogenetic signal assessment, emergence of amino acid substitutions, and Bayesian evolutionary rate estimation in eight successive fortnights since the virus emergence.All observed phylogenetic signals were very low and tree topologies were in agreement with those signals. However, after four months of evolution, it was possible to identify regions revealing an incipient viral lineage formation despite the low phylogenetic signal, since fortnight 3. Finally, the SARS‐CoV‐2 evolutionary rate for regions nsp3 and S, the ones presenting greater variability, was estimated as 1.37 x 10‐3 and 2.19 x 10‐3 substitution/site/year, respectively.In conclusion, results from this work about the variable diversity of crucial viral regions and determination of the evolutionary rate are consequently decisive to understand essential features of viral emergence. In turn, findings may allow the first time characterization of the evolutionary rate of S protein, crucial for vaccine development.Fil: Pereson, Matías J.. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Virología; ArgentinaFil: Mojsiejczuk, Laura Noelia. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay; ArgentinaFil: Martínez, Alfredo P.. Centro de Educaciones Médicas e Investigación Clínica "Norberto Quirno"; ArgentinaFil: Flichman, Diego Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas en Retrovirus y Sida. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas en Retrovirus y Sida; ArgentinaFil: García, Gabriel Hugo. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Virología; ArgentinaFil: Di Lello, Federico Alejandro. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay; ArgentinaVeterinary and Human Toxicology2020-09info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/115890Pereson, Matías J.; Mojsiejczuk, Laura Noelia; Martínez, Alfredo P.; Flichman, Diego Martin; García, Gabriel Hugo; et al.; Phylogenetic analysis of SARS‐CoV‐2 in the first few months since its emergence; Veterinary and Human Toxicology; Journal of Medical Virology; 9-2020; 1-270146-6615CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/10.1002/jmv.26545info:eu-repo/semantics/altIdentifier/doi/10.1002/jmv.26545info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-nd/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:49:41Zoai:ri.conicet.gov.ar:11336/115890instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 09:49:41.975CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Phylogenetic analysis of SARS‐CoV‐2 in the first few months since its emergence
title Phylogenetic analysis of SARS‐CoV‐2 in the first few months since its emergence
spellingShingle Phylogenetic analysis of SARS‐CoV‐2 in the first few months since its emergence
Pereson, Matías J.
SARS-COV-2
PHYLOGENY
EVOLUTION
EVOLUTIONARY RATE
COVID-19
title_short Phylogenetic analysis of SARS‐CoV‐2 in the first few months since its emergence
title_full Phylogenetic analysis of SARS‐CoV‐2 in the first few months since its emergence
title_fullStr Phylogenetic analysis of SARS‐CoV‐2 in the first few months since its emergence
title_full_unstemmed Phylogenetic analysis of SARS‐CoV‐2 in the first few months since its emergence
title_sort Phylogenetic analysis of SARS‐CoV‐2 in the first few months since its emergence
dc.creator.none.fl_str_mv Pereson, Matías J.
Mojsiejczuk, Laura Noelia
Martínez, Alfredo P.
Flichman, Diego Martin
García, Gabriel Hugo
Di Lello, Federico Alejandro
author Pereson, Matías J.
author_facet Pereson, Matías J.
Mojsiejczuk, Laura Noelia
Martínez, Alfredo P.
Flichman, Diego Martin
García, Gabriel Hugo
Di Lello, Federico Alejandro
author_role author
author2 Mojsiejczuk, Laura Noelia
Martínez, Alfredo P.
Flichman, Diego Martin
García, Gabriel Hugo
Di Lello, Federico Alejandro
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv SARS-COV-2
PHYLOGENY
EVOLUTION
EVOLUTIONARY RATE
COVID-19
topic SARS-COV-2
PHYLOGENY
EVOLUTION
EVOLUTIONARY RATE
COVID-19
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv During the first months of SARS‐CoV‐2 evolution in a new host, contrasting hypotheses have been proposed about the way the virus has evolved and diversified worldwide. The aim of this study was to perform a comprehensive evolutionary analysis to describe the human outbreak and the evolutionary rate of different genomic regions of SARS‐CoV‐2.The molecular evolution in nine genomic regions of SARS‐CoV‐2 was analyzed using three different approaches: phylogenetic signal assessment, emergence of amino acid substitutions, and Bayesian evolutionary rate estimation in eight successive fortnights since the virus emergence.All observed phylogenetic signals were very low and tree topologies were in agreement with those signals. However, after four months of evolution, it was possible to identify regions revealing an incipient viral lineage formation despite the low phylogenetic signal, since fortnight 3. Finally, the SARS‐CoV‐2 evolutionary rate for regions nsp3 and S, the ones presenting greater variability, was estimated as 1.37 x 10‐3 and 2.19 x 10‐3 substitution/site/year, respectively.In conclusion, results from this work about the variable diversity of crucial viral regions and determination of the evolutionary rate are consequently decisive to understand essential features of viral emergence. In turn, findings may allow the first time characterization of the evolutionary rate of S protein, crucial for vaccine development.
Fil: Pereson, Matías J.. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Virología; Argentina
Fil: Mojsiejczuk, Laura Noelia. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay; Argentina
Fil: Martínez, Alfredo P.. Centro de Educaciones Médicas e Investigación Clínica "Norberto Quirno"; Argentina
Fil: Flichman, Diego Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas en Retrovirus y Sida. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas en Retrovirus y Sida; Argentina
Fil: García, Gabriel Hugo. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Virología; Argentina
Fil: Di Lello, Federico Alejandro. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay; Argentina
description During the first months of SARS‐CoV‐2 evolution in a new host, contrasting hypotheses have been proposed about the way the virus has evolved and diversified worldwide. The aim of this study was to perform a comprehensive evolutionary analysis to describe the human outbreak and the evolutionary rate of different genomic regions of SARS‐CoV‐2.The molecular evolution in nine genomic regions of SARS‐CoV‐2 was analyzed using three different approaches: phylogenetic signal assessment, emergence of amino acid substitutions, and Bayesian evolutionary rate estimation in eight successive fortnights since the virus emergence.All observed phylogenetic signals were very low and tree topologies were in agreement with those signals. However, after four months of evolution, it was possible to identify regions revealing an incipient viral lineage formation despite the low phylogenetic signal, since fortnight 3. Finally, the SARS‐CoV‐2 evolutionary rate for regions nsp3 and S, the ones presenting greater variability, was estimated as 1.37 x 10‐3 and 2.19 x 10‐3 substitution/site/year, respectively.In conclusion, results from this work about the variable diversity of crucial viral regions and determination of the evolutionary rate are consequently decisive to understand essential features of viral emergence. In turn, findings may allow the first time characterization of the evolutionary rate of S protein, crucial for vaccine development.
publishDate 2020
dc.date.none.fl_str_mv 2020-09
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
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://hdl.handle.net/11336/115890
Pereson, Matías J.; Mojsiejczuk, Laura Noelia; Martínez, Alfredo P.; Flichman, Diego Martin; García, Gabriel Hugo; et al.; Phylogenetic analysis of SARS‐CoV‐2 in the first few months since its emergence; Veterinary and Human Toxicology; Journal of Medical Virology; 9-2020; 1-27
0146-6615
CONICET Digital
CONICET
url http://hdl.handle.net/11336/115890
identifier_str_mv Pereson, Matías J.; Mojsiejczuk, Laura Noelia; Martínez, Alfredo P.; Flichman, Diego Martin; García, Gabriel Hugo; et al.; Phylogenetic analysis of SARS‐CoV‐2 in the first few months since its emergence; Veterinary and Human Toxicology; Journal of Medical Virology; 9-2020; 1-27
0146-6615
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/10.1002/jmv.26545
info:eu-repo/semantics/altIdentifier/doi/10.1002/jmv.26545
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Veterinary and Human Toxicology
publisher.none.fl_str_mv Veterinary and Human Toxicology
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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