Omicron waves in Argentina: dynamics of SARS-CoV-2 lineages BA.1, BA.2 and the emerging BA.2.12.1 and BA.4/BA.5

Autores
Toro, Rosana; Proyecto PAIS Working Group
Año de publicación
2023
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The COVID-19 pandemic has lately been driven by Omicron. This work aimed to study the dynamics of SARS-CoV-2 Omicron lineages during the third and fourth waves of COVID-19 in Argentina. Molecular surveillance was performed on 3431 samples from Argentina, between EW44/2021 and EW31/2022. Sequencing, phylogenetic and phylodynamic analyses were performed. A differential dynamic between the Omicron waves was found. The third wave was associated with lineage BA.1, characterized by a high number of cases, very fast displacement of Delta, doubling times of 3.3 days and a low level of lineage diversity and clustering. In contrast, the fourth wave was longer but associated with a lower number of cases, initially caused by BA.2, and later by BA.4/BA.5, with doubling times of about 10 days. Several BA.2 and BA.4/BA.5 sublineages and introductions were detected, although very few clusters with a constrained geographical distribution were observed, suggesting limited transmission chains. The differential dynamic could be due to waning immunity and an increase in population gatherings in the BA.1 wave, and a boosted population (for vaccination or recent prior immunity for BA.1 infection) in the wave caused by BA2/BA.4/BA.5, which may have limited the establishment of the new lineages.
La lista completa de autores que integran el documento puede consultarse en el archivo.
Facultad de Ciencias Exactas
Materia
Biología
Ciencias Médicas
SARS-CoV-2
Omicron
Variants
Evolution
South America
Dynamics
BA.1
BA.2
BA.4
BA.5
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by/4.0/
Repositorio
SEDICI (UNLP)
Institución
Universidad Nacional de La Plata
OAI Identificador
oai:sedici.unlp.edu.ar:10915/153022
Acceder
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repository_id_str 1329
network_name_str SEDICI (UNLP)
spelling Omicron waves in Argentina: dynamics of SARS-CoV-2 lineages BA.1, BA.2 and the emerging BA.2.12.1 and BA.4/BA.5Toro, RosanaProyecto PAIS Working GroupBiologíaCiencias MédicasSARS-CoV-2OmicronVariantsEvolutionSouth AmericaDynamicsBA.1BA.2BA.4BA.5The COVID-19 pandemic has lately been driven by Omicron. This work aimed to study the dynamics of SARS-CoV-2 Omicron lineages during the third and fourth waves of COVID-19 in Argentina. Molecular surveillance was performed on 3431 samples from Argentina, between EW44/2021 and EW31/2022. Sequencing, phylogenetic and phylodynamic analyses were performed. A differential dynamic between the Omicron waves was found. The third wave was associated with lineage BA.1, characterized by a high number of cases, very fast displacement of Delta, doubling times of 3.3 days and a low level of lineage diversity and clustering. In contrast, the fourth wave was longer but associated with a lower number of cases, initially caused by BA.2, and later by BA.4/BA.5, with doubling times of about 10 days. Several BA.2 and BA.4/BA.5 sublineages and introductions were detected, although very few clusters with a constrained geographical distribution were observed, suggesting limited transmission chains. The differential dynamic could be due to waning immunity and an increase in population gatherings in the BA.1 wave, and a boosted population (for vaccination or recent prior immunity for BA.1 infection) in the wave caused by BA2/BA.4/BA.5, which may have limited the establishment of the new lineages.La lista completa de autores que integran el documento puede consultarse en el archivo.Facultad de Ciencias Exactas2023info: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/10915/153022enginfo:eu-repo/semantics/altIdentifier/issn/1999-4915info:eu-repo/semantics/altIdentifier/doi/10.3390/v15020312info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International (CC BY 4.0)reponame:SEDICI (UNLP)instname:Universidad Nacional de La Platainstacron:UNLP2025-09-29T11:39:34Zoai:sedici.unlp.edu.ar:10915/153022Institucionalhttp://sedici.unlp.edu.ar/Universidad públicaNo correspondehttp://sedici.unlp.edu.ar/oai/snrdalira@sedici.unlp.edu.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:13292025-09-29 11:39:34.402SEDICI (UNLP) - Universidad Nacional de La Platafalse
dc.title.none.fl_str_mv Omicron waves in Argentina: dynamics of SARS-CoV-2 lineages BA.1, BA.2 and the emerging BA.2.12.1 and BA.4/BA.5
title Omicron waves in Argentina: dynamics of SARS-CoV-2 lineages BA.1, BA.2 and the emerging BA.2.12.1 and BA.4/BA.5
spellingShingle Omicron waves in Argentina: dynamics of SARS-CoV-2 lineages BA.1, BA.2 and the emerging BA.2.12.1 and BA.4/BA.5
Toro, Rosana
Biología
Ciencias Médicas
SARS-CoV-2
Omicron
Variants
Evolution
South America
Dynamics
BA.1
BA.2
BA.4
BA.5
title_short Omicron waves in Argentina: dynamics of SARS-CoV-2 lineages BA.1, BA.2 and the emerging BA.2.12.1 and BA.4/BA.5
title_full Omicron waves in Argentina: dynamics of SARS-CoV-2 lineages BA.1, BA.2 and the emerging BA.2.12.1 and BA.4/BA.5
title_fullStr Omicron waves in Argentina: dynamics of SARS-CoV-2 lineages BA.1, BA.2 and the emerging BA.2.12.1 and BA.4/BA.5
title_full_unstemmed Omicron waves in Argentina: dynamics of SARS-CoV-2 lineages BA.1, BA.2 and the emerging BA.2.12.1 and BA.4/BA.5
title_sort Omicron waves in Argentina: dynamics of SARS-CoV-2 lineages BA.1, BA.2 and the emerging BA.2.12.1 and BA.4/BA.5
dc.creator.none.fl_str_mv Toro, Rosana
Proyecto PAIS Working Group
author Toro, Rosana
author_facet Toro, Rosana
Proyecto PAIS Working Group
author_role author
author2 Proyecto PAIS Working Group
author2_role author
dc.subject.none.fl_str_mv Biología
Ciencias Médicas
SARS-CoV-2
Omicron
Variants
Evolution
South America
Dynamics
BA.1
BA.2
BA.4
BA.5
topic Biología
Ciencias Médicas
SARS-CoV-2
Omicron
Variants
Evolution
South America
Dynamics
BA.1
BA.2
BA.4
BA.5
dc.description.none.fl_txt_mv The COVID-19 pandemic has lately been driven by Omicron. This work aimed to study the dynamics of SARS-CoV-2 Omicron lineages during the third and fourth waves of COVID-19 in Argentina. Molecular surveillance was performed on 3431 samples from Argentina, between EW44/2021 and EW31/2022. Sequencing, phylogenetic and phylodynamic analyses were performed. A differential dynamic between the Omicron waves was found. The third wave was associated with lineage BA.1, characterized by a high number of cases, very fast displacement of Delta, doubling times of 3.3 days and a low level of lineage diversity and clustering. In contrast, the fourth wave was longer but associated with a lower number of cases, initially caused by BA.2, and later by BA.4/BA.5, with doubling times of about 10 days. Several BA.2 and BA.4/BA.5 sublineages and introductions were detected, although very few clusters with a constrained geographical distribution were observed, suggesting limited transmission chains. The differential dynamic could be due to waning immunity and an increase in population gatherings in the BA.1 wave, and a boosted population (for vaccination or recent prior immunity for BA.1 infection) in the wave caused by BA2/BA.4/BA.5, which may have limited the establishment of the new lineages.
La lista completa de autores que integran el documento puede consultarse en el archivo.
Facultad de Ciencias Exactas
description The COVID-19 pandemic has lately been driven by Omicron. This work aimed to study the dynamics of SARS-CoV-2 Omicron lineages during the third and fourth waves of COVID-19 in Argentina. Molecular surveillance was performed on 3431 samples from Argentina, between EW44/2021 and EW31/2022. Sequencing, phylogenetic and phylodynamic analyses were performed. A differential dynamic between the Omicron waves was found. The third wave was associated with lineage BA.1, characterized by a high number of cases, very fast displacement of Delta, doubling times of 3.3 days and a low level of lineage diversity and clustering. In contrast, the fourth wave was longer but associated with a lower number of cases, initially caused by BA.2, and later by BA.4/BA.5, with doubling times of about 10 days. Several BA.2 and BA.4/BA.5 sublineages and introductions were detected, although very few clusters with a constrained geographical distribution were observed, suggesting limited transmission chains. The differential dynamic could be due to waning immunity and an increase in population gatherings in the BA.1 wave, and a boosted population (for vaccination or recent prior immunity for BA.1 infection) in the wave caused by BA2/BA.4/BA.5, which may have limited the establishment of the new lineages.
publishDate 2023
dc.date.none.fl_str_mv 2023
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
Articulo
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info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://sedici.unlp.edu.ar/handle/10915/153022
url http://sedici.unlp.edu.ar/handle/10915/153022
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/issn/1999-4915
info:eu-repo/semantics/altIdentifier/doi/10.3390/v15020312
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by/4.0/
Creative Commons Attribution 4.0 International (CC BY 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
Creative Commons Attribution 4.0 International (CC BY 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
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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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