Phylogenetic reconstruction of hCoV-19 (SARS-CoV-2) genomes has been essential for characterizing viral evolution across South America, where regional transmission and lineage persistence have shaped the pandemic landscape. A South America-focused phylogenetic tree highlights patterns of diversification within the continent while situating them within the global evolutionary framework through the inclusion of selected external genomes.
This analysis spans the pandemic timeline from 2020 to the present, capturing both early lineage emergence and more recent evolutionary trends. Time-resolved sequencing data allow the tree to reflect changes in lineage composition across successive waves of infection.
The most recent portion of the phylogenetic tree is primarily composed of viruses belonging to XFG.3.4.1, which currently dominate newly submitted genomes from South America. These lineages form prominent clusters at the tips of the tree, consistent with ongoing transmission. Alongside these, XFG and XFG.3.3.1 remain present, indicating continued diversification within Omicron-derived lineages.
The structure of the tree traces how these lineages branch from earlier variants, illustrating the temporal accumulation of mutations and supporting evolutionary inference based on molecular clock models.
Recent submissions to GISAID show that Chile, Brazil, and Ecuador are the leading sources of hCoV-19 (SARS-CoV-2) genome data from South America in the current period. High sequencing contributions from these countries enhance the resolution of phylogenetic clusters and improve the ability to investigate regional transmission patterns.
To preserve global context, a limited number of genomes from outside South America are included, providing reference points for shared ancestry and cross-continental spread.
A South America-focused hCoV-19 (SARS-CoV-2) phylogenetic tree provides a framework for understanding how viral evolution and regional transmission intersect. It strengthens genomic surveillance efforts, improves interpretation of lineage dynamics, and places South American viral diversity within the broader global context of hCoV-19 (SARS-CoV-2) evolution.
