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

CAROLINA TORRES; MERCEDES NABAES JODAR, DOLORES ACUÑA ; ROMINA MICAELA ZAMBRANA MONTAÑO, ANDRÉS CARLOS ALBERTO CULASSO; ARIEL FERNANDO AMADIO; PAULA AULICINO; SANTIAGO CEBALLOS; MARCO CACCIABUE; HUMBERTO DEBAT; MARÍA JOSÉ DUS SANTOS; MARÍA FLORENCIA EBERHARDT; CARLOS ESPUL; FABIÁN FAY; MARÍA AILÉN FERNÁNDEZ; FRANCO FERNÁNDEZ; FLORENCIA FERRINI; ADRIANA ANGÉLICA GIRI ; MARÍA INES GISMONDI; STEPHANIE GOYA; JOSÉ MATÍAS IRAZOQUI , GUIDO ALBERTO KÖNIG; VIVIANA LEIVA; HORACIO LUCERO; NATHALIE MARQUEZ; CRISTINA NARDI; BELÉN ORTIZ; LUIS PIANCIOLA, CAROLINA BEATRIZ PINTOS; ANDREA FABIANA PUEBLA; CAROLINA VICTORIA RASTELLINI; ALEJANDRO EZEQUIEL ROJAS; JAVIER SFALCIN; ARIEL SUÁREZ, ESTEFANÍA TITTARELLI; ROSANA TORO; GABRIELA VANINA VILLANOVA; MARÍA CECILIA ZIEHM; MARÍA CARLA ZIMMERMANN; SEBASTIÁN ZUNINO; PROYECTO PAIS WORKING GROUP; LAURA VALINOTTO AND MARIANA VIEGAS; AGUSTINA CERRI ; AGUSTINA CERRI , ELISA BOLATTI

Viruses

MDPI

Lugar: Basel; Año: 2023

1999-4915

Abstract: The COVID-19 pandemic has lately been driven by Omicron. This work aimed to studythe dynamics of SARS-CoV-2 Omicron lineages during the third and fourth waves of COVID-19in Argentina. Molecular surveillance was performed on 3431 samples from Argentina, betweenEW44/2021 and EW31/2022. Sequencing, phylogenetic and phylodynamic analyses were performed.A differential dynamic between the Omicron waves was found. The third wave was associated withlineage BA.1, characterized by a high number of cases, very fast displacement of Delta, doubling timesof 3.3 days and a low level of lineage diversity and clustering. In contrast, the fourth wave was longerbut associated with a lower number of cases, initially caused by BA.2, and later by BA.4/BA.5, withdoubling times of about 10 days. Several BA.2 and BA.4/BA.5 sublineages and introductions weredetected, although very few clusters with a constrained geographical distribution were observed,suggesting limited transmission chains. The differential dynamic could be due to waning immunityand an increase in population gatherings in the BA.1 wave, and a boosted population (for vaccinationor recent prior immunity for BA.1 infection) in the wave caused by BA2/BA.4/BA.5, which may havelimited the establishment of the new lineages.