OMICRON WAVES IN ARGENTINA: DYNAMICS OF SARS-COV-2 LINEAGES BA.1, BA.2 AND THE EMERGING BA.2.12.1 AND BA.4

TORRES C (AUTORA PARA CORRESPONDENCIA); NABAES JODAR M; ACUÑA D; ACEVEDO RM; AMADIO A; AULICINO P; BLAZQUEZ AC; CEBALLOS S; DEBAT H; DUS SANTOS MJ; EBERHARDT MF; ESPUL C; FALASCHI A; FAY F; FERNANDEZ A; FERNANDEZ F; FERRINI F; GALLEGO F; GIRI A; GISMONDI MI; GOYA S; GRAMUNDI I; IRAZOQUI M; KONIG G; LEIVA V; LUCERO H; MARQUEZ N; NARDI C; NIELSEN C; PIANCIOLA L; PUEBLA A; RASTELLINI C; SFALCIN J; SUAREZ A; TITTARELLI E; VILLANOVA V; ZIMMERMAN C; ZUNINO S; PROYECTO PAIS; VALINOTTO L; VIEGAS M (AUTORA PARA CORRESPONDENCIA)

Workshop; 26th International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME); 2022

The COVID-19 pandemic has strongly impacted all populations worldwide and was recently driven by Omicron, causing new waves of infections in almost all regions of the world. South America suffered the Omicron wave almost simultaneously with other regions in December 2021-March 2022. Even though more than 4 million SARS-CoV-2 Omicron genomes have been uploaded to GISAID, only 1.7% belong to South America and of these, very few have been included in evolutionary analyses of circulating viruses in the region. This work aimed to study the dynamics of SARS-CoV-2 lineages circulation during the third and fourth waves of COVID-19 in Argentina and to add information about its evolutionary behaviour.Surveillance of SARS-CoV-2 variants was performed on a total of 2984 samples from the capital city and 13 provinces of Argentina belonging to individuals without travel history during the epidemiological weeks (EW) 44/2021 to EW22/2022, covering the third and fourth waves of the COVID-19 pandemic in the country. The surveillance strategy was based on Sanger sequencing of a Spike coding region (that allows the identification of signature mutations associated with variants) and on whole-genome sequencing (Illumina and Nanopore platforms) (~1100 complete genomes of the total sampling). Omicron lineage BA.1 was first detected in EW50/2021, reaching 72.5% of new cases two weeks later (EW52/2021), producing a record number of cases by mid-January and completely displacing Delta in EW4/2022. While lineage BA.2 was detected for the first time in EW7/2022 and reached 51.2% in EW14/2022, displacing BA.1 more slowly than when BA.1 displaced Delta. More recently, driving the fourth wave together with BA.2, the emerging lineages BA.2.12.1 and BA.4/BA.5 have also been detected (EW15-16/2022). Different introductions were observed for BA.2.12.1, reaching 24.0% of detections in EW22/2022. Analyses of the evolutionary and epidemiological dynamics of the main groups observed are in progress.The surveillance strategy implemented over the last seven months in Argentina allowed us to describe the introduction and establishment of the main SARS-CoV-2 Omicron lineages in the third and fourth waves of the COVID-19 pandemic in the country, adding information about the expansion of emerging lineages BA.2.12.1 and BA.4/BA.5 in South America.