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

MDPI

Año: 2023 vol. 15

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.