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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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Autores principales: Torres, Carolina, Nabaes Jodar, Mercedes, Acuña, Dolores, Montaño, Romina Micaela Zambrana, Culasso, Andrés Carlos Alberto, Amadio, Ariel Fernando, Aulicino, Paula, Ceballos, Santiago, Cacciabue, Marco, Debat, Humberto, Dus Santos, María José, Eberhardt, María Florencia, Espul, Carlos, Fay, Fabián, Fernández, María Ailén, Fernández, Franco, Muñoz, Juan Manuel Fernandez, Ferrini, Florencia, Gallego, Fernando, Giri, Adriana Angélica, Cerri, Agustina, Bolatti, Elisa, Gismondi, María Ines, Goya, Stephanie, Gramundi, Iván, Irazoqui, José Matías, König, Guido Alberto, Leiva, Viviana, Lucero, Horacio, Marquez, Nathalie, Nardi, Cristina, Ortiz, Belén, Pianciola, Luis, Pintos, Carolina Beatriz, Puebla, Andrea Fabiana, Rastellini, Carolina Victoria, Rojas, Alejandro Ezequiel, Sfalcin, Javier, Suárez, Ariel, Tittarelli, Estefanía, Toro, Rosana, Villanova, Gabriela Vanina, Ziehm, María Cecilia, Zimmermann, María Carla, Zunino, Sebastián, Valinotto, Laura, Viegas, Mariana
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9965068/
https://www.ncbi.nlm.nih.gov/pubmed/36851525
http://dx.doi.org/10.3390/v15020312
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author Torres, Carolina
Nabaes Jodar, Mercedes
Acuña, Dolores
Montaño, Romina Micaela Zambrana
Culasso, Andrés Carlos Alberto
Amadio, Ariel Fernando
Aulicino, Paula
Ceballos, Santiago
Cacciabue, Marco
Debat, Humberto
Dus Santos, María José
Eberhardt, María Florencia
Espul, Carlos
Fay, Fabián
Fernández, María Ailén
Fernández, Franco
Muñoz, Juan Manuel Fernandez
Ferrini, Florencia
Gallego, Fernando
Giri, Adriana Angélica
Cerri, Agustina
Bolatti, Elisa
Gismondi, María Ines
Goya, Stephanie
Gramundi, Iván
Irazoqui, José Matías
König, Guido Alberto
Leiva, Viviana
Lucero, Horacio
Marquez, Nathalie
Nardi, Cristina
Ortiz, Belén
Pianciola, Luis
Pintos, Carolina Beatriz
Puebla, Andrea Fabiana
Rastellini, Carolina Victoria
Rojas, Alejandro Ezequiel
Sfalcin, Javier
Suárez, Ariel
Tittarelli, Estefanía
Toro, Rosana
Villanova, Gabriela Vanina
Ziehm, María Cecilia
Zimmermann, María Carla
Zunino, Sebastián
Valinotto, Laura
Viegas, Mariana
author_facet Torres, Carolina
Nabaes Jodar, Mercedes
Acuña, Dolores
Montaño, Romina Micaela Zambrana
Culasso, Andrés Carlos Alberto
Amadio, Ariel Fernando
Aulicino, Paula
Ceballos, Santiago
Cacciabue, Marco
Debat, Humberto
Dus Santos, María José
Eberhardt, María Florencia
Espul, Carlos
Fay, Fabián
Fernández, María Ailén
Fernández, Franco
Muñoz, Juan Manuel Fernandez
Ferrini, Florencia
Gallego, Fernando
Giri, Adriana Angélica
Cerri, Agustina
Bolatti, Elisa
Gismondi, María Ines
Goya, Stephanie
Gramundi, Iván
Irazoqui, José Matías
König, Guido Alberto
Leiva, Viviana
Lucero, Horacio
Marquez, Nathalie
Nardi, Cristina
Ortiz, Belén
Pianciola, Luis
Pintos, Carolina Beatriz
Puebla, Andrea Fabiana
Rastellini, Carolina Victoria
Rojas, Alejandro Ezequiel
Sfalcin, Javier
Suárez, Ariel
Tittarelli, Estefanía
Toro, Rosana
Villanova, Gabriela Vanina
Ziehm, María Cecilia
Zimmermann, María Carla
Zunino, Sebastián
Valinotto, Laura
Viegas, Mariana
author_sort Torres, Carolina
collection PubMed
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.
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spelling pubmed-99650682023-02-26 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 Torres, Carolina Nabaes Jodar, Mercedes Acuña, Dolores Montaño, Romina Micaela Zambrana Culasso, Andrés Carlos Alberto Amadio, Ariel Fernando Aulicino, Paula Ceballos, Santiago Cacciabue, Marco Debat, Humberto Dus Santos, María José Eberhardt, María Florencia Espul, Carlos Fay, Fabián Fernández, María Ailén Fernández, Franco Muñoz, Juan Manuel Fernandez Ferrini, Florencia Gallego, Fernando Giri, Adriana Angélica Cerri, Agustina Bolatti, Elisa Gismondi, María Ines Goya, Stephanie Gramundi, Iván Irazoqui, José Matías König, Guido Alberto Leiva, Viviana Lucero, Horacio Marquez, Nathalie Nardi, Cristina Ortiz, Belén Pianciola, Luis Pintos, Carolina Beatriz Puebla, Andrea Fabiana Rastellini, Carolina Victoria Rojas, Alejandro Ezequiel Sfalcin, Javier Suárez, Ariel Tittarelli, Estefanía Toro, Rosana Villanova, Gabriela Vanina Ziehm, María Cecilia Zimmermann, María Carla Zunino, Sebastián Valinotto, Laura Viegas, Mariana Viruses Article 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. MDPI 2023-01-22 /pmc/articles/PMC9965068/ /pubmed/36851525 http://dx.doi.org/10.3390/v15020312 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Torres, Carolina
Nabaes Jodar, Mercedes
Acuña, Dolores
Montaño, Romina Micaela Zambrana
Culasso, Andrés Carlos Alberto
Amadio, Ariel Fernando
Aulicino, Paula
Ceballos, Santiago
Cacciabue, Marco
Debat, Humberto
Dus Santos, María José
Eberhardt, María Florencia
Espul, Carlos
Fay, Fabián
Fernández, María Ailén
Fernández, Franco
Muñoz, Juan Manuel Fernandez
Ferrini, Florencia
Gallego, Fernando
Giri, Adriana Angélica
Cerri, Agustina
Bolatti, Elisa
Gismondi, María Ines
Goya, Stephanie
Gramundi, Iván
Irazoqui, José Matías
König, Guido Alberto
Leiva, Viviana
Lucero, Horacio
Marquez, Nathalie
Nardi, Cristina
Ortiz, Belén
Pianciola, Luis
Pintos, Carolina Beatriz
Puebla, Andrea Fabiana
Rastellini, Carolina Victoria
Rojas, Alejandro Ezequiel
Sfalcin, Javier
Suárez, Ariel
Tittarelli, Estefanía
Toro, Rosana
Villanova, Gabriela Vanina
Ziehm, María Cecilia
Zimmermann, María Carla
Zunino, Sebastián
Valinotto, Laura
Viegas, Mariana
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
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_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_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
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9965068/
https://www.ncbi.nlm.nih.gov/pubmed/36851525
http://dx.doi.org/10.3390/v15020312
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