EMERGENCE AND SPREAD OF SARS-COV-2 GAMMA VARIANT IN ARGENTINA

ZAMBRANA MONTAÑO, ROMINA MICAELA; NABAES JODAR, MERCEDES ; GOYA, STEPHANIE ; ACUÑA, DOLORES ; ACEVEDO, RAÚL MAXIMILIANO ; AMADIO, ARIEL ; BRUSÉS, BETINA ; CEBALLOS, SANTIAGO ; DEBAT, HUMBERTO ; EBERHARDT, MARÍA FLORENCIA ; FERNÁNDEZ, AILÉN ; FERNÁNDEZ, FRANCO ; FORMICHELLI, LAURA ; GALLEGO, FERNANDO ; GRAMUNDI, IVÁN ; IRAZOQUI, MATÍAS ; KÖNIG, GUIDO ; LORENZINI CAMPOS, MELINA ; LUCERO, HORACIO ; MARQUEZ, NATHALIE ; MAZZEO, MELINA ; MUSSIN, JAVIER; NARDI, CRISTINA ; ORIA, GRISELDA ; OUSSET, JULIA ; PIANCIOLA, LUIS ; PINTOS, CAROLINA ; PUEBLA, ANDREA ; RASTELLINI, CAROLINA ; ROJAS, EZEQUIEL ; VALINOTTO, LAURA ; ZIEHN, CECILIA ; PROYECTO PAIS; TORRES, CAROLINA (SHARED LAST AUTHORSHIP); VIEGAS, MARIANA (SHARED LAST AUTHORSHIP)

Conferencia; Virus Genomics and Evolution 2022; 2022

The SARS-CoV-2 pandemic was principally associated with the spread of the Variant of Concern (VOC) and variants of interest (VOIs), which have been defined by the WHO. Gamma variant (lineage P.1 and its derivatives sublineages), first detected in Manaus (Brazil) in late 2020, was one of the dominant variants in South America in 2021 causing a large number of infected people due to its transmission advantage.In Argentina, Gamma was detected in February 2021 for the first time and replaced other previously circulating lineages in the country. Therefore, the Argentinean second wave, which peaked around May 2021, was characterized by the introduction and rapid spread of Gamma and its sublineages in the country. We sequenced 625 SARS-CoV-2 whole-genomes and performed phylogenetic analyses (Maximum Likelihood method, IQ-TREE v2.1 software) to identify introduction events and diversification process of the Gamma variant during this second epidemic wave in Argentina. Sequences came from samples of individuals diagnosed with COVID-19 from February to December 2021 and were obtained with Oxford Nanopore or Illumina platforms, in the context of the molecular surveillance implemented by PAIS Consortium in Argentina. Phylogenetic analysis showed that the P.1 lineage was predominant throughout the second wave in Argentina, as well as the P.1.15 and P.1.2 sublineages. Followed by Gamma sublineages P.1.13, P.1.14 and P.1.17.Several introductions of the Gamma variant to Argentina were observed in the phylogenetic tree of lineage P.1. Large groups containing Argentinean sequences from north to south of the country were observed, which suggests a wide local transmission and diversification of common transmission chains. In addition, clades that contain sequences from one or few provinces were observed, suggesting a more regionalized local transmission. In both cases, The Argentine sequences were grouped with sequences from other countries of the South American region (such as Brazil and Paraguay), and with sequences from the USA.For the P.1.15 sublineage, a transmission pattern similar to that of the P.1 lineage was observed. However, for sublineage P.1.2, clusters included sequences from only a few Argentinean provinces, which suggests a more limited geographical dispersion.In conclusion, Gamma was the main variant in the second wave of COVID-19 in Argentina, originated from several introductions and showing a wide distribution, with circumscribed and extended transmission chains throughout the country. These results reveal the impact of the regional circulation of SARS-CoV-2 variants on the epidemiology of Argentina in the second wave.