Genomic Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2, Colombia.

Publisher: National Center for Infectious Diseases, Centers for Disease Control and Prevention (CDC) Country of Publication: United States NLM ID: 9508155 Publication Model: Print Cited Medium: Internet ISSN: 1080-6059 (Electronic) Linking ISSN: 10806040 NLM ISO Abbreviation: Emerg Infect Dis Subsets: MEDLINE

Original Publication: Atlanta, GA : National Center for Infectious Diseases, Centers for Disease Control and Prevention (CDC), [1995-

Genome, Viral* ; Phylogeny*; COVID-19/*epidemiology ; COVID-19/*virology ; Genomics/*methods ; SARS-CoV-2/*genetics; Colombia/epidemiology ; Humans ; Reproducibility of Results

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.

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MC_PC_19012 United Kingdom MRC_ Medical Research Council; MR/R015600/1 United Kingdom MRC_ Medical Research Council; MR/R024855/1 United Kingdom MRC_ Medical Research Council

Keywords: COVID-19; Colombia; SARS; SARS-CoV-2; coronavirus; coronavirus disease; genome sequencing; phylogenomics; respiratory infections; severe acute respiratory syndrome coronavirus 2; viruses; zoonoses

Date Created: 20201121 Date Completed: 20201204 Latest Revision: 20220126

20240105

PMC7706936

10.3201/eid2612.202969

33219646