Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina

Studies about the evolution of SARS-CoV-2 lineages in different backgrounds such as naive populations are still scarce, especially from South America. This work aimed to study the introduction and diversification pattern of SARS-CoV-2 during the first year of the COVID-19 pandemic in the Northwestern Argentina (NWA) region and to analyze the evolutionary dynamics of the main lineages found. In this study, we analyzed a total of 260 SARS-CoV-2 whole-genome sequences from Argentina, belonging to the Provinces of Jujuy, Salta, and Tucumán, from March 31st, 2020, to May 22nd, 2021, which covered the full first wave and the early second wave of the COVID-19 pandemic in Argentina. In the first wave, eight lineages were identified: B.1.499 (76.9%), followed by N.5 (10.2%), B.1.1.274 (3.7%), B.1.1.348 (3.7%), B.1 (2.8%), B.1.600 (0.9%), B.1.1.33 (0.9%) and N.3 (0.9%). During the early second wave, the first-wave lineages were displaced by the introduction of variants of concern (VOC) (Alpha, Gamma), or variants of interest (VOI) (Lambda, Zeta, Epsilon) and other lineages with more limited distribution. Phylodynamic analyses of the B.1.499 and N.5, the two most prevalent lineages in the NWA, revealed that the rate of evolution of lineage N.5 (7.9 × 10−4 substitutions per site per year, s/s/y) was a ∼40% faster than that of lineage B.1.499 (5.6 × 10−4 s/s/y), although both are in the same order of magnitude than other non-VOC lineages. No mutations associated with a biological characteristic of importance were observed as signatures markers of the phylogenetic groups established in Northwestern Argentina, however, single sequences in non-VOC lineages did present mutations of biological importance or associated with VOCs as sporadic events, showing that many of these mutations could emerge from circulation in the general population. This study contributed to the knowledge about the evolution of SARS-CoV-2 in a pre-vaccination and without post-exposure immunization period.Instituto de Patología VegetalFil: Zambrana Montaño, Romina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular; ArgentinaFil: Zambrana Montaño, Romina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Culasso, Andrés Carlos Alberto. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular; ArgentinaFil: Culasso, Andrés Carlos Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Fernandez, Franco Daniel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Fernandez, Franco Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Marquez, Nathalie. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Marquez, Nathalie. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Debat, Humberto Julio. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Salmerón, Mariana. Laboratorio de Salud Pública; ArgentinaFil: Zamora, Ana María. Laboratorio de Salud Pública; ArgentinaFil: Ruíz de Huidobro, Gustavo. Laboratorio de Salud Pública; ArgentinaFil: Costas, Dardo. Laboratorio de Salud Pública; ArgentinaFil: Alabarse, Graciela. Laboratorio de Salud Pública; ArgentinaFil: Charre, Miguel Alejandro. Laboratorio Central de Salud Pública, San Salvador de Jujuy; ArgentinaFil: Fridman, Ariel David. Laboratorio Central de Salud Pública. San Salvador de Jujuy; ArgentinaFil: Mamani, Claudia. Laboratorio Central de Salud Pública. San Salvador de Jujuy; ArgentinaFil: Vaca, Fabiana. Laboratorio Central de Salud Pública. San Salvador de Jujuy; ArgentinaFil: Maza Diaz, Claudia. Laboratorio Central de Salud Pública. San Salvador de Jujuy; ArgentinaFil: Raskovsky, Viviana. Hospital Señor del Milagro. Laboratorio de Virus Respiratorios y Neurovirosis; ArgentinaFil: Lavaque, Esteban. Hospital Señor del Milagro. Laboratorio de Virus Respiratorios y Neurovirosis; ArgentinaFil: Lesser, Veronica. Hospital Señor del Milagro. Laboratorio de Virus Respiratorios y Neurovirosis; ArgentinaFil: Cajal, Pamela. Hospital Señor del Milagro. Laboratorio de Virus Respiratorios y Neurovirosis; ArgentinaFil: Agüero, Fernanda. Hospital Señor del Milagro. Laboratorio de Virus Respiratorios y Neurovirosis; ArgentinaFil: Calvente, Cintia. Hospital Señor del Milagro. Laboratorio de Virus Respiratorios y Neurovirosis; ArgentinaFil: Torres, Carolina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular; ArgentinaFil: Torres, Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Viegas, Mariana. Hospital de Niños Dr. Ricardo Gutiérrez. Laboratorio de Virología; Argentin