Characterizing SARS-CoV-2 genome diversity circulating in South American countries: signatures of potentially emergent lineages?

Muñoz, Marina; Patiño, Luz H.; Ballesteros, Nathalia; Paniz-Mondolfi, Alberto; Ramírez, Juan David

Objectives To evaluate the genomic diversity and geographic distribution of SARS-CoV-2 lineages currently circulating in South America (SA). Methods SARS-CoV-2 lineages reported from South American countries were analyzed from a public dataset of 5597 genome assemblies. Polymorphisms in the main open reading frames were identified and compared to those present in the main lineages of epidemiology concern: B.1.1.7 (from UK) and B.1.351 (from South Africa). Results A total of 169 circulating lineages across 16 South American countries were identified, revealing a predominant circulation of the major lineage B, the one with the greatest diversity and broadest geographic distribution. Sixteen lineages were selected to be comprehensively analyzed because are predominant in the region. Two lineages of concern report were remarkably identified: P.1 recognized as the Brazilian variant (with 94 genomes) and B.1.1.7 the UK variant (with 28 genomes), both displayed 33 polymorphisms compared to the reference genome, the highest number among analyzed genomes. While the most of other lineages circulating in SA displayed 24 or less polymorphisms compared to the reference strain. A high number of polymorphisms were detected in the evaluated lineages with a limited number of common variable positions amongst them, in agreement with the profiles identified in the main lineages of epidemiology concern. Conclusions The ever-increasing genetic diversity of SARS-CoV-2 continues to lead to the emergence of novel lineages. Different variants and lineages are now present across SA with the presence of major lineage B mostly. The circulation of variants as P.1 and B.1.1.7 in different countries as well as the elevated number of polymorphisms highlighted the importance of continuing with the genomic surveillance to determine introduction events, identify transmission chains, trace emergence and help to implement successful prevention, vaccination and control strategies.