DYNAMIC OF SARS-COV-2 LAMBDA VARIANT (LINEAGE C.37) IN ARGENTINA

NABAES JODAR, MERCEDES S.; MOJSIEJCZUK, LAURA; TORRES, C; ACUÑA, DOLORES; ALEXAY, SOFÍA; AULICINO, PAULA; GOYA, STEPHANIE; KÖNIG, GUIDO; CONSORCIO INTERINSTITUCIONAL PARA LA SECUENCIACIÓN DEL GENOMA Y ESTUDIOS GENÓMICOS DE SARS-COV-2 (PROYECTO PAIS); VIEGAS, MARIANA

Conferencia; Virus Genomics and Evolution (Virtual Conference); 2021

Wellcome Genome Campus, UK

Mercedes S Nabaes Jodar (1,2)*, Laura Mojsiejczuk (2,3)*, *equally contributing authors. 1.Molecular surveillance of SARS-CoV-2 focused on VOC/VOI monitoring was implemented in Argentina by PAIS Consortium in late 2020. The surveillance strategy was mainly based on the detection of signature mutations in the Spike protein by Sanger sequencing in weekly collected samples. The Buenos Aires Metropolitan Area (AMBA), the most densely populated area in the country, has been the epicenter of the COVID-19 epidemic in Argentina. Except for Beta and Delta, all SARS-CoV-2 variants described so far were found in the AMBA, as well as other locations in the country. Here, we describe the emergence and spread of the Lambda variant in the AMBA. In addition, a phylodynamic analysis was performed to identify the genetic relationships, temporal, and geographic spread of Lambda local and global isolates. The signature pattern associated with Lambda (S_L452Q, S_F490S, and the synonymous mutation S_c2169t) was found in 295 out of 1524 sequences collected between EW-44/2020 and EW-17/2021 in the AMBA. First detected on January 20, Lambda frequency increased steadily since mid-February and reached a value of 44.7% by the end of April, becoming with Gamma the dominant variants. Complete genomes were obtained in 74 samples and combined with sequences from the GISAID database to perform phylogenetic and phylodynamic analyses. Overall, the Maximum Likelihood tree of Lambda showed highly supported clades including sequences from the same country. However, the basal relationship between clades could not be solved with confidence. The Bayesian phylodynamic analysis placed the common ancestor of Lambda in Peru (posterior probability 0.88) in November 2020. From there, the lineage spread to other South American countries, mainly Chile and Argentina. Argentinean sequences were located in five main groups, evidencing multiple introductions to the country: four of them from Peru and one from Chile. The common ancestors of the two major and widespread Argentinean groups were dated in late December and early January 2021, respectively. Four out of the five Argentinean clades have common ancestors in the AMBA, and from there spread to other regions of the country. In conclusion, molecular surveillance and phylodynamic reconstruction indicated that the introduction and spread of Lambda overlapped with a peak of COVID-19 cases in Argentina that occurred after the year-end holidays. Once had established in the AMBA, the lineage spread to other regions inside the country and abroad, contributing to the second wave in South America.