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

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,...

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Detalles Bibliográficos
Autores: Toro, Rosana, Proyecto PAIS Working Group
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2023
País:Argentina
Institución:Universidad Nacional de La Plata
Repositorio:SEDICI (UNLP)
Idioma:inglés
OAI Identifier:oai:sedici.unlp.edu.ar:10915/153022
Acceso en línea:http://sedici.unlp.edu.ar/handle/10915/153022
Access Level:acceso abierto
Palabra clave:Biología
Ciencias Médicas
SARS-CoV-2
Omicron
Variants
Evolution
South America
Dynamics
BA.1
BA.2
BA.4
BA.5
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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:UNLP2024-05-08T13:18:21Zoai: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:13292024-05-08 13:18:21.279SEDICI (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
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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format article
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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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instname_str Universidad Nacional de La Plata
instacron_str UNLP
institution UNLP
reponame_str SEDICI (UNLP)
collection SEDICI (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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