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; Proyecto PAIS Working Group,; Valinotto, Laura; Viegas, Mariana

doi:10.3390/v15020312

Open AccessArticle

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

by

Carolina Torres

^1,2,*

,

Mercedes Nabaes Jodar

^2,3,

Dolores Acuña

^2,3,

Romina Micaela Zambrana Montaño

^1,2,

Andrés Carlos Alberto Culasso

^1,2

,

Ariel Fernando Amadio

^2,4

,

Paula Aulicino

^2,5,

Santiago Ceballos

⁶,

Marco Cacciabue

⁷,

Humberto Debat

⁸

,

María José Dus Santos

^9,10

,

María Florencia Eberhardt

^2,4,

Carlos Espul

¹¹,

Fabián Fay

¹²,

María Ailén Fernández

¹³,

Franco Fernández

⁸,

Juan Manuel Fernandez Muñoz

¹⁴

,

Florencia Ferrini

¹⁵,

Fernando Gallego

⁶,

Adriana Angélica Giri

¹⁶

,

Agustina Cerri

¹⁶,

Elisa Bolatti

¹⁶

,

María Ines Gismondi

^7,17,

Stephanie Goya

³,

Iván Gramundi

⁶,

José Matías Irazoqui

^2,4

,

Guido Alberto König

⁷,

Viviana Leiva

¹¹,

Horacio Lucero

¹⁸,

Nathalie Marquez

⁸

,

Cristina Nardi

⁶,

Belén Ortiz

¹¹,

Luis Pianciola

¹³

,

Carolina Beatriz Pintos

¹³,

Andrea Fabiana Puebla

⁷,

Carolina Victoria Rastellini

¹³,

Alejandro Ezequiel Rojas

⁶,

Javier Sfalcin

¹²,

Ariel Suárez

¹⁹,

Estefanía Tittarelli

¹⁹,

Rosana Toro

²⁰,

Gabriela Vanina Villanova

^2,21

,

María Cecilia Ziehm

¹³,

María Carla Zimmermann

¹⁵

,

Sebastián Zunino

^17,22,

Proyecto PAIS Working Group

^23,†,

Laura Valinotto

^2,3 and

Mariana Viegas

^2,3,*

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¹

Instituto de Investigaciones en Bacteriología y Virología Molecular (IbaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires 1113, Argentina

²

Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires 1425, Argentina

³

Laboratorio de Virología Hospital de Niños Dr. Ricardo Gutiérrez, Ciudad Autónoma de Buenos Aires 1425, Argentina

⁴

Instituto de Investigación de la Cadena Láctea (IDICAL) INTA-CONICET, Rafaela 2300, Argentina

⁵

Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría “Prof. Juan P. Garrahan”, Ciudad Autónoma de Buenos Aires 1245, Argentina

⁶

Hospital Regional Ushuaia; Universidad Nacional de Tierra del Fuego, Antártida e Islas del Atlántico Sur, UNTDF y CADIC-CONICET, Ushuaia 9410, Argentina

⁷

Instituto de Biotecnología/Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Hurlingham 1686, Argentina

⁸

Instituto de Patología Vegetal-Centro de Investigaciones Agropecuarias Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba 5020, Argentina

⁹

Instituto de Virología e Innovaciones Tecnológicas (INTA-CONICET), Hurlingham 1686, Argentina

¹⁰

Laboratorio de Diagnóstico-UNIDAD COVID- Universidad Nacional de Hurlingham, Hurlingham 1688, Argentina

¹¹

Laboratorio de Salud Pública, Godoy Cruz 5501, Argentina

¹²

CIBIC Laboratorio, Rosario 2000, Argentina

¹³

Laboratorio Central Neuquén, Ministerio de Salud de la Provincia del Neuquén, Neuquén 8302, Argentina

¹⁴

Instituto de Medicina y Biología Experimental de Cuyo (IMBECU—CONICET), Mendoza 5500, Argentina

¹⁵

Laboratorio de Medicina Genómica, Facultad de Medicina, Universidad Nacional del Nordeste, Corrientes 3400, Argentina

¹⁶

IBR-CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario 2000, Argentina

¹⁷

Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina

¹⁸

Instituto de Medicina Regional, Resistencia 3500, Argentina

¹⁹

Departamento de Biología y Genética Molecular, IACA Laboratorios, Bahía Blanca 8000, Argentina

²⁰

Laboratorio de salud pública, Facultad de Ciencias Exactas, UNLP, La Plata 1900, Argentina

²¹

Laboratorio de Biotecnología Acuática, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Centro Científico Tecnológico y Educativo Acuario del río Paraná, Rosario 2000, Argentina

²²

Laboratorio de Virología Molecular, Hospital Blas L. Dubarry, Mercedes 6600, Argentina

²³

PAIS Working Group, Ministerio de Ciencia Tecnología e Innovación, Ciudad Autónoma de Buenos Aires 1425, Argentina

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^*

Authors to whom correspondence should be addressed.

^†

PAIS Working Group at http://pais.qb.fcen.uba.ar/about.php.

Viruses 2023, 15(2), 312; https://doi.org/10.3390/v15020312

Submission received: 30 December 2022 / Revised: 14 January 2023 / Accepted: 18 January 2023 / Published: 22 January 2023

(This article belongs to the Special Issue What SARS-CoV-2 Variants Have Taught Us: Evolutionary Challenges of RNA Viruses)

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Abstract

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.

Keywords: SARS-CoV-2; Omicron; variants; evolution; South America; dynamics; BA.1; BA.2; BA.4; BA.5

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MDPI and ACS Style

Torres, C.; Nabaes Jodar, M.; Acuña, D.; Montaño, R.M.Z.; Culasso, A.C.A.; Amadio, A.F.; Aulicino, P.; Ceballos, S.; Cacciabue, M.; Debat, H.; et al. 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. Viruses 2023, 15, 312. https://doi.org/10.3390/v15020312

AMA Style

Torres C, Nabaes Jodar M, Acuña D, Montaño RMZ, Culasso ACA, Amadio AF, Aulicino P, Ceballos S, Cacciabue M, Debat H, et al. 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. Viruses. 2023; 15(2):312. https://doi.org/10.3390/v15020312

Chicago/Turabian Style

Torres, Carolina, Mercedes Nabaes Jodar, Dolores Acuña, Romina Micaela Zambrana Montaño, Andrés Carlos Alberto Culasso, Ariel Fernando Amadio, Paula Aulicino, Santiago Ceballos, Marco Cacciabue, Humberto Debat, and et al. 2023. "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" Viruses 15, no. 2: 312. https://doi.org/10.3390/v15020312

APA Style

Torres, C., Nabaes Jodar, M., Acuña, D., Montaño, R. M. Z., Culasso, A. C. A., Amadio, A. F., Aulicino, P., Ceballos, S., Cacciabue, M., Debat, H., Dus Santos, M. J., Eberhardt, M. F., Espul, C., Fay, F., Fernández, M. A., Fernández, F., Muñoz, J. M. F., Ferrini, F., Gallego, F., ... Viegas, M. (2023). 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. Viruses, 15(2), 312. https://doi.org/10.3390/v15020312

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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

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