GENOMIC CHARACTERIZATION OF SARS-COV-2 IN NORTHWESTERN ARGENTINA DURING THE FIRST WAVE OF THE COVID-19 PANDEMIC

ZAMBRANA MONTAÑO R ; FERNÁNDEZ F; CULASSO A; MARQUEZ N; DEBAT H; SALMERÓN MB; ZAMORA AM; RUÍZ DE HUIDOBRO G; COSTAS DE; ALABARSE G; CHARRE MA; FRIDMAN AD; MAMANI C; VACA F; RASKOVSKY V; LAVAQUE E; LESSER V; CAJAL P; AGÜERO F; TORRES C (ULTIMA AUTORIA COMPARTIDA); VIEGAS M (ULTIMA AUTORIA COMPARTIDA)

Congreso; 2nd Women in Bioinformatics & Data Science LA Conference; 2021

The SARS-CoV-2 is the etiological agent of the coronavirus disease 2019 (COVID-19), diagnosed for the first time in Argentina on March 3, 2020. To understand its evolution process and spread throughout the country, the PAIS Consortium was created through the COVID-19 Unit (Ministry of Science, Technology and Innovation). The SARS-CoV-2 has been classified in lineages, named using an alphanumeric code (Pango nomenclature system).This study aimed to identify the SARS-CoV-2 lineages that circulated in Northwest Argentina during the first wave, and to investigate further into the origin and evolution of the relevant groups. Samples from Jujuy (9), Salta (32) and Tucumán (30) from individuals diagnosed with SARS-CoV-2 infection from March to September 2020, were analyzed. Complete genome sequences were obtained using the ARTIC protocol in a MinION platform. Phylogenetic analysis was performed (Maximum Likelihood method, IQ-TREE v2.1 software) to assign lineages and to study their diversification process.Three lineages were found: B.1.499 (94.4%), B.1 (4.2%) and B.1.1.33 (1,4%). For the B.1.499, several viral introductions to the region and the formation of local transmission clusters, both within provinces and regionally, were found. This lineage was predominant throughout Argentina during the first wave, showing a marked regionalization, compatible with travel restrictions and quarantine measures. Besides, three sequences were assigned to the B.1 lineage (two from Salta and one from Tucumán) and one sequence was assigned to B.1.1.33 lineage, from an individual with international travel history.Moreover, as part of the natural evolution of SARS-CoV-2, nucleotide mutations were found among different regions of the viral genome of some sequences, including the region that encodes for the Spike protein.Our research constitutes a base for future analyzes that will allow to study how the introduction of new lineages and variants impact on the epidemiological patterns in Argentina and neighboring countries.