Phylogenetic analysis has become central to monitoring hCoV-19 (SARS-CoV-2) since the beginning of the pandemic. In Latin America and the Caribbean, a region characterized by vast geographic diversity and major urban centers, genomic surveillance offers critical insight into how lineages circulate and evolve. A Latin America and the Caribbean–focused phylogenetic reconstruction captures viral diversity across countries such as Anguilla, Antigua and Barbuda, Argentina, Aruba, Bahamas, Barbados, Belize,Bermuda, Bolivia, Brazil, British Virgin Islands, Cayman Islands, Chile, Colombia, Costa Rica, Cuba, Curaçao, Dominica, Dominican Republic, Ecuador, El Salvador,French Guiana, Grenada, Guadeloupe, Guatemala, Guyana, Haiti, Honduras, Jamaica,Martinique, Mexico, Montserrat, Netherland Antilles, Nicaragua, Panama, Paraguay, Peru, Puerto Rico, Saint Kitts and Nevis, Saint Lucia, Saint Vincent and the Grenadines,Sint Maarten, Suriname, Trinidad and Tobago, Turks and Caicos, Uruguay and Venezuela.
From the first documented cases in 2020 through the most recent genome submissions, the tree reflects the dynamic interplay between regional transmission and global viral movement. By incorporating sampling dates, the phylogeny becomes time-resolved, enabling researchers to trace how successive waves—Alpha, Gamma, Delta, Omicron, and their descendants—reshaped the continent’s genomic landscape.
Latin America and the Caribbean has played notable roles in the emergence and expansion of several hCoV-19 (SARS-CoV-2) lineages. Within the phylogenetic tree, clusters associated with past and present variants demonstrate how certain lineages achieved regional dominance before being replaced by more transmissible or immune-evasive descendants.
Recent sequences predominantly group within XFG.* variant, forming distinct tip clusters that reflect ongoing circulation. The branching structure documents mutation accumulation and provides a framework for estimating divergence times. These patterns help clarify lineage turnover, persistence in specific regions, and cross-border spread within the continent.
The strength of a Latin America and the Caribbean–focused phylogeny lies in its geographic representation. Genome submissions from multiple countries improve cluster definition and increase confidence in transmission inferences. Brazil and Chile are contributors that account for the majority of newly deposited genomes in the present analytical window. At the same time, the inclusion of curated global reference sequences ensures that the regional analysis remains embedded within the broader pandemic context, allowing identification of introduction events and international connectivity.
By aligning evolutionary data with geography and time, a Latin America and the Caribbean–centered phylogenetic tree transforms raw genomic sequences into actionable epidemiological insight. It highlights regional transmission corridors, documents lineage replacement events, and supports evidence-based public health planning. Sustained sequencing and data integration will remain essential for tracking hCoV-19 (SARS-CoV-2) evolution and strengthening genomic surveillance across Latin America and the Caribbean.
