The Lambda Variant in Argentina: Analyzing the Evolution and Spread of SARS-CoV-2 Lineage C.37

Abstract

The second wave of COVID-19 occurred in South America in early 2021 and was mainly driven by Gamma and Lambda variants. In this study, we aimed to describe the emergence and local genomic diversity of the SARS-CoV-2 Lambda variant in Argentina, from its initial entry into the country until its detection ceased. Molecular surveillance was conducted on 9356 samples from Argentina between October 2020 and April 2022, and sequencing, phylogenetic, and phylogeographic analyses were performed. Our findings revealed that the Lambda variant was first detected in Argentina in January 2021 and steadily increased in frequency until it peaked in April 2021, with continued detection throughout the year. Phylodynamic analyses showed that at least 18 introductions of the Lambda variant into the country occurred, with nine of them having evidence of onward local transmission. The spatial–-temporal reconstruction showed that Argentine clades were associated with Lambda sequences from Latin America and suggested an initial diversification in the Metropolitan Area of Buenos Aires before spreading to other regions in Argentina. Genetic analyses of genome sequences allowed us to describe the mutational patterns of the Argentine Lambda sequences and detect the emergence of rare mutations in an immunocompromised patient. Our study highlights the importance of genomic surveillance in identifying the introduction and geographical distribution of the SARS-CoV-2 Lambda variant, as well as in monitoring the emergence of mutations that could be involved in the evolutionary leaps that characterize variants of concern.

Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean

“…Colombia was the main origin of Lambda lineages circulating in Central America, which might be related to the dominance of Lambda in the country’s Pacific region 24 , and the whole Mu epidemic, originating from Colombia, was much more effective in spreading towards the north than to the south. Argentina and Chile were also observed as important routes of Lambda spreading towards the Caribbean and Mexico, which agreed with previous studies investigating the Lambda epidemic wave in these two countries 25 , 26 . Another identified pattern that emerged within South America is the preferential viral migration among neighboring countries located in the western side (Colombia, Ecuador, and Peru) or the eastern side (Brazil, Argentina, Paraguay, and Uruguay) of the Andes; while Chile, Bolivia and Venezuela seem to be strongly connected with both sides.…”

Ready for new waves: optimizing SARS-CoV-2 variants monitoring in pooled samples with droplet digital PCR

“…The dynamic nature of COVID-19 pandemic is characterized by the emergence and succession of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, categorized as variants of concern (VOCs), variants of interest (VOIs), and, more recently, variants being monitored (VBM) (1)(2)(3)(4)(5).…”