Genomic Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2, Colombia

Laiton-Donato, Katherine; Villabona-Arenas, Christian Julián; Usme-Ciro, José A.; Franco-Muñoz, Carlos; Álvarez-Díaz, Diego A.; Villabona-Arenas, Liz Stephany; Echeverría-Londoño, Susy; Cucunubá, Zulma M.; Franco-Sierra, Nicolás D.; Flórez, Astrid C.; Ferro, Carolina; Ajami, Nadim J.; Walteros, Diana Marcela; Prieto, Franklin; Durán, Carlos Andrés; Ospina-Martínez, Martha Lucia; Mercado-Reyes, Marcela

Coronavirus disease (COVID-19) in Colombia was first diagnosed in a traveler arriving from Italy on February 26, 2020. However, limited data are available on the origins and number of introductions of COVID-19 into the country. We sequenced the causative agent of COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), from 43 clinical samples we collected, along with another 79 genome sequences available from Colombia. We investigated the emergence and importation routes for SARS-CoV-2 into Colombia by using epidemiologic, historical air travel, and phylogenetic observations. Our study provides evidence of multiple introductions, mostly from Europe, and documents >12 lineages. Phylogenetic findings validate the lineage diversity, support multiple importation events, and demonstrate the evolutionary relationship of epidemiologically linked transmission chains. Our results reconstruct the early evolutionary history of SARS-CoV-2 in Colombia and highlight the advantages of genome sequencing to complement COVID-19 outbreak investigations.