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Emerg Infect Dis
. 2020 Dec;26(12):2854-2862.
doi: 10.3201/eid2612.202969.
Genomic Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2, Colombia
Katherine Laiton-Donato, Christian Juli?n Villabona-Arenas, Jos? A Usme-Ciro, Carlos Franco-Mu?oz, Diego A ?lvarez-D?az, Liz Stephany Villabona-Arenas, Susy Echeverr?a-Londo?o, Zulma M Cucunub?, Nicol?s D Franco-Sierra, Astrid C Fl?rez, Carolina Ferro, Nadim J Ajami, Diana Marcela Walteros, Franklin Prieto, Carlos Andr?s Dur?n, Martha Lucia Ospina-Mart?nez, Marcela Mercado-Reyes
- PMID: 33219646
- DOI: 10.3201/eid2612.202969
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.
Keywords: COVID-19; Colombia; SARS; SARS-CoV-2; coronavirus; coronavirus disease; genome sequencing; phylogenomics; respiratory infections; severe acute respiratory syndrome coronavirus 2; viruses; zoonoses.