Genomic Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2, Colombia
Katherine Laiton‐Donato, Christian Julián Villabona‐Arenas, José A. Usme-Ciro, Carlos Franco-Muñoz, Diego A. Álvarez-Díaz, Liz Stephany Villabona-Arenas, Susy Echeverría-Londoño, Zulma M. Cucunubá, Nicolás D. Franco‐Sierra, Astrid Carolina Floréz, Carolina Ferro, Nadim J. Ajami, Diana Marcela Walteros Acero, Franklin Prieto, Carlos Andrés Durán, Martha Lucía Ospina Martínez, Marcela Mercado
Abstract
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.