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

Emerging Infectious Diseases
Katherine Laiton-DonatoM. M. Mercado-Reyes

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.

References

Jan 1, 1985·Journal of Molecular Evolution·M HasegawaT Yano
Jul 24, 2002·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Jan 19, 2010·Bioinformatics·Heng Li, Richard Durbin
Oct 2, 2015·Systematic Biology·Thu-Hien ToOlivier Gascuel
Jan 18, 2018·Virus Evolution·Pavel SagulenkoRichard A Neher
May 24, 2018·Bioinformatics·James HadfieldRichard A Neher
Nov 14, 2018·Bioinformatics·Shifu ChenJia Gu
Dec 14, 2018·Nature Microbiology·Nathan D GrubaughKristian G Andersen
Jan 30, 2020·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·Victor M CormanChristian Drosten
Feb 6, 2020·Molecular Biology and Evolution·Bui Quang MinhRobert Lanfear
Mar 3, 2020·The Lancet Global Health·Joel HellewellRosalind M Eggo
Mar 27, 2020·Journal of Travel Medicine·Darlan Da S CandidoNuno R Faria
Mar 28, 2020·Science·Moritz U G KraemerSamuel V Scarpino
Mar 31, 2020·Journal of Medical Virology·Andrés E CastilloJorge Fernández
Apr 15, 2020·The New England Journal of Medicine·Daniel F GudbjartssonKari Stefansson
Apr 17, 2020·Nature Medicine·Xi HeGabriel M Leung
Apr 17, 2020·Virus Evolution·John-Sebastian EdenUNKNOWN 2019-nCoV Study Group
Apr 29, 2020·The American Journal of Tropical Medicine and Hygiene·Junyao LiDebiao Song
Jun 10, 2020·International Journal for Equity in Health·Fabiana Ribeiro, Anja Leist
Jul 17, 2020·Nature Microbiology·Andrew RambautOliver G Pybus
Jul 25, 2020·Science·Darlan S CandidoNuno Rodrigues Faria

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Citations

Jan 14, 2021·Annals of Clinical Microbiology and Antimicrobials·Whilken NovoaHector Serrano-Coll
Jan 16, 2021·The Lancet Infectious Diseases·Simona FiorentiniArnaldo Caruso
Jul 6, 2021·Current Opinion in Environmental Science & Health·R Sivaranjanee, P Senthil Kumar
Jul 16, 2021·Frontiers in Medicine·Katherine Laiton-DonatoMarcela Mercado-Reyes
Jun 30, 2021·Journal of Medical Virology·Eduardo Juscamayta-LópezRonnie Gavilán
Aug 18, 2021·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Katherine Laiton-DonatoMarcela Mercado-Reyes
Oct 5, 2021·Archives of Virology·Sindy P Buitrago, Diego Garzón-Ospina

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Datasets Mentioned

BETA
MN908947.3

Methods Mentioned

BETA
reverse transcription PCR
nucleic acid extraction
GISAID

Software Mentioned

NextStrain
TreeTime
fastp
BBMap
MAFFT
IQ
TREE
Porechop
Nanopolish
GISAID

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