• 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 CAROLINA; NABAES JODAR, MERCEDES SOLEDAD; DUS SANTOS MARIA JOSE; CONSORCIO PAIS

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

Omicron waves in Argentina: dynamics of SARS-CoV-2 lineages BA.1, BA.2 and the emerging BA.2.12.1 and BA.4Torres C.* (1,2), Nabaes Jodar M. (2,3), Acuña D. (2,3), Acevedo R. M. (4), Amadio A. (2,5), Aulicino P. (2,6), Blazquez A. C. (7), Ceballos S. (8), Debat H (9), Dus santos M. J. (10,11), Eberhardt M. F. (2,5), Espul C. (12), Falaschi A. (12), Fay F. (13), Fernández A. (14), Fernández F. (9), Ferrini F. (15), Gallego F. (8), Giri A. (16), Gismondi M. I. (17,18); Goya S (3), Gramundi I. (8), Irazoqui M. (2,5), König G. (17), Leiva V. (22), Lucero H. (19), Marquez N. (9), Nardi C. (8), Nielsen R. (7), Pianciola L. (14), Puebla A. (17), Rastellini C. (14), Sfalcin J. (13), Suárez A. (20), Tittarelli E. (20), Villanova V. (21), Zimmerman C. (15), Zunino S. (18,23), Proyecto PAIS (24), Valinotto L. (2,3), Viegas M. (2,3)(1) Universidad de Buenos Aires Facultad de Farmacia y Bioquímica Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), CABA, Argentina.(2) Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina.(3) Laboratorio de Virología Hospital de Niños Dr. Ricardo Gutiérrez, CABA, Argentina.(4) Instituto de Botánica del Nordeste (CONICET-UNNE), Corrientes, Argentina.(5) Instituto de Investigación de la Cadena Láctea (IDICAL) INTA-CONICET. Rafaela, provincia de Santa Fe Argentina.(6) Laboratorio de Biología Celular y Retrovirus. Hospital de Pediatría "Prof. Juan P. Garrahan", CABA, Argentina.(7) Laboratorio Generis. Caleta Olivia, provincia de Santa Cruz, Argentina.(8) Hospital Regional Ushuaia; Universidad Nacional de Tierra del Fuego, Antártida e Islas del Atlántico Sur; UNTDF y CADIC-CONICET. Ushuaia, provincia de Tierra del Fuego, Argentina.(9) Instituto de Patología Vegetal-Centro de Investigaciones Agropecuarias Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, provincia de Córdoba, Argentina.(10) Instituto de Virología e Innovaciones Tecnológicas (INTA-CONICET), Hurlingham, provincia de Buenos Aires, Argentina.(11) Laboratorio de Diagnóstico-UNIDAD COVID- Universidad Nacional de Hurlingham, Hurlingham, provincia de Buenos Aires, Argentina.(12) Dirección de epidemiología y Red de Laboratorios del Ministerio de Salud de la provincia de Mendoza. Mendoza, provincia de Mendoza, Argentina.(13) CIBIC Laboratorio. Rosario, provincia de Santa Fe, Argentina.(14) Laboratorio Central de la ciudad de Neuquén, Ministerio de Salud. Neuquén, provincia de Neuquén, Argentina.(15) Laboratorio de Medicina Genómica, Facultad de Medicina, Universidad Nacional del Nordeste. Corrientes, provincia de Corrientes, Argentina.(16) IBR-CONICET, Universidad Nacional de Rosario; Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario. Rosario, provincia de Santa Fe, Argentina.(17) Instituto de Biotecnología/Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET). Hurlingham, provincia de Buenos Aires, Argentina.(18) Universidad Nacional de Luján, Departamento de Ciencias Básicas. Luján, provincia de Buenos Aires, Argentina.(19) Instituto de Medicina Regional. Resistencia, provincia de Chaco, Argentina.(20) Departamento de Biología y Genética Molecular; IACA Laboratorios. Bahía Blanca, provincia de Buenos Aires, Argentina.(21) Laboratorio Mixto de Biotecnología Acuática. Rosario, provincia de Santa Fe, Argentina.(22) Laboratorio de Salud Pública. Ciudad de Mendoza, provincia de Mendoza, Argentina.(23) Laboratorio de Virología Molecular, Hospital Blas L. Dubarry. Mercedes, provincia de Buenos Aires, Argentina.(24) Ministerio de Ciencia Tecnología e Innovación, Argentina. http://pais.qb.fcen.uba.ar/. AbstractThe 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.