Genomic epidemiology of severe acute respiratory syndrome coronavirus 2, Colombia

Laiton-Donato K.,
Villabona-Arenas C.J.,
Usme-Ciro J.A.,
Franco-Muñoz C.,
Álvarez-Díaz D.A.,
Villabona-Arenas L.S.,
Echeverría-Londoño S.,
Cucunubá Z.M.,
Franco-Sierra N.D.,
Flórez A.C.,
Ferro C.,
Ajami N.J.,
Walteros D.M.,
Prieto F.,
Durán C.A.,
Ospina-Martínez M.L.,
Mercado-Reyes M.
Document Type
Source Title
Emerging Infectious Diseases
Centers for Disease Control and Prevention (CDC)


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 SARSCoV-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. © 2020 Centers for Disease Control and Prevention (CDC). All rights reserved.

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Index Keywords

Article; asymptomatic disease; Colombia; coronavirus disease 2019; coughing; disease severity; disease surveillance; fever; gene sequence; genetic distance; genetic variability; genomics; high throughput sequencing; human; molecular evolution; phylogeny; reverse transcription polymerase chain reaction; sequence alignment; Severe acute respiratory syndrome coronavirus 2; single nucleotide polymorphism; throat culture; virus infectivity; World Health Organization; contact examination; coronavirus disease 2019; genetic epidemiology; nonhuman; pandemic; real time reverse transcription polymerase chain reaction; species diversity; virus genome; virus transmission; epidemiology; genetics; genomics; phylogeny; procedures; reproducibility; virology; RNA directed DNA polymerase; Colombia; COVID-19; Genome, Viral; Genomics; Humans; Phylogeny; Reproducibility of Results; SARS-CoV-2