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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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; Zambrana Montaño, Romina Micaela; 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; Fernandez Muñoz, Juan Manuel; Ferrini, Florencia; Gallego, Fernando; Giri, Adriana Angélica; Cerri, Agustina; Bolatti, Elisa María; 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
URI: http://hdl.handle.net/2133/25429
Date: 2023-01-22

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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