Genomic epidemiology of SARS-CoV-2 variants during the first two years of the pandemic in Colombia

Cinthy Jimenez-Silva; Ricardo Rivero; Jordan Douglas; Remco Bouckaert; Ch. Julian Villabona-Arenas; Katherine E. Atkins; Bertha Gastelbondo; Alfonso Calderon; Camilo Guzman; Daniel Echeverri-De la Hoz; Marina Muñoz; Nathalia Ballesteros; Sergio Castañeda; Luz H. Patiño; Angie Ramirez; Nicolas Luna; Alberto Paniz-Mondolfi; Hector Serrano-Coll; Juan David Ramirez; Salim Mattar; Alexei J. Drummond

doi:10.1038/s43856-023-00328-3

Genomic epidemiology of SARS-CoV-2 variants during the first two years of the pandemic in Colombia

Cinthy Jimenez-Silva, Ricardo Rivero, Jordan Douglas, Remco Bouckaert, Ch. Julian Villabona-Arenas, Katherine E. Atkins, Bertha Gastelbondo, Alfonso Calderon, Camilo Guzman, Daniel Echeverri-De la Hoz, Marina Muñoz, Nathalia Ballesteros, Sergio Castañeda, Luz H. Patiño, Angie Ramirez, Nicolas Luna, Alberto Paniz-Mondolfi, Hector Serrano-Coll, Juan David Ramirez, Salim MattarAlexei J. Drummond

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Abstract / Description of output

The emergence of highly transmissible SARS-CoV-2 variants has led to surges in cases and the need for global genomic surveillance. While some variants rapidly spread worldwide, other variants only persist nationally. There is a need for more fine-scale analysis to understand transmission dynamics at a country scale. For instance, the Mu variant of interest, also known as lineage B.1.621, was first detected in Colombia and was responsible for a large local wave but only a few sporadic cases elsewhere.

Original language	English
Article number	97
Number of pages	12
Journal	Communications Medicine
Volume	3
Issue number	1
DOIs	https://doi.org/10.1038/s43856-023-00328-3
Publication status	Published - 13 Jul 2023

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Genomic epidemiology_JIMENEZ-SILVA_DOA22062023_VOR_CC-BYFinal published version, 1.96 MBLicence: Creative Commons: Attribution (CC-BY)

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HIV-1 acquisition and the future of prevention strategies: deciphering the eclipse phase through modelling and phylogenetics - HIV ECLIPSE
Atkins, K.
EU government bodies
1/03/18 → 30/11/24
Project: Research

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Jimenez-Silva, C., Rivero, R., Douglas, J., Bouckaert, R., Villabona-Arenas, C. J., Atkins, K. E., Gastelbondo, B., Calderon, A., Guzman, C., Echeverri-De la Hoz, D., Muñoz, M., Ballesteros, N., Castañeda, S., Patiño, L. H., Ramirez, A., Luna, N., Paniz-Mondolfi, A., Serrano-Coll, H., Ramirez, J. D., ... Drummond, A. J. (2023). Genomic epidemiology of SARS-CoV-2 variants during the first two years of the pandemic in Colombia. Communications Medicine, 3(1), Article 97. https://doi.org/10.1038/s43856-023-00328-3

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title = "Genomic epidemiology of SARS-CoV-2 variants during the first two years of the pandemic in Colombia",

abstract = "The emergence of highly transmissible SARS-CoV-2 variants has led to surges in cases and the need for global genomic surveillance. While some variants rapidly spread worldwide, other variants only persist nationally. There is a need for more fine-scale analysis to understand transmission dynamics at a country scale. For instance, the Mu variant of interest, also known as lineage B.1.621, was first detected in Colombia and was responsible for a large local wave but only a few sporadic cases elsewhere.",

author = "Cinthy Jimenez-Silva and Ricardo Rivero and Jordan Douglas and Remco Bouckaert and Villabona-Arenas, {Ch. Julian} and Atkins, {Katherine E.} and Bertha Gastelbondo and Alfonso Calderon and Camilo Guzman and {Echeverri-De la Hoz}, Daniel and Marina Mu{\~n}oz and Nathalia Ballesteros and Sergio Casta{\~n}eda and Pati{\~n}o, {Luz H.} and Angie Ramirez and Nicolas Luna and Alberto Paniz-Mondolfi and Hector Serrano-Coll and Ramirez, {Juan David} and Salim Mattar and Drummond, {Alexei J.}",

note = "This work is supported by the Marsden grant 18-UOA-096 from the Royal Society of New Zealand, Colombia{\textquoteright}s Science Ministry (Minciencias), BPIN 20200000100090. This project was funded by the Universidad del Rosario in the framework of its strategic plan RUTA2025. Thanks to President and the University Council for leading the strategic projects (JR). We also thank the Colombian network for SARS-CoV-2 genomic surveillance led by the National Institute of Health (INS). C.J.V.-A. and K.E.A. were funded by the European Research Council (ERC) Starting Grant 757688 (to K.E.A.). We thank the National Genomic Surveillance Network of the National Institute of Health (Red de Vigilancia Gen{\'o}mica del Instituto Nacional de Salud) for generating and curating the SARS-COV-2 data that made this study possible.",

year = "2023",

month = jul,

day = "13",

doi = "10.1038/s43856-023-00328-3",

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Jimenez-Silva, C, Rivero, R, Douglas, J, Bouckaert, R, Villabona-Arenas, CJ, Atkins, KE, Gastelbondo, B, Calderon, A, Guzman, C, Echeverri-De la Hoz, D, Muñoz, M, Ballesteros, N, Castañeda, S, Patiño, LH, Ramirez, A, Luna, N, Paniz-Mondolfi, A, Serrano-Coll, H, Ramirez, JD, Mattar, S & Drummond, AJ 2023, 'Genomic epidemiology of SARS-CoV-2 variants during the first two years of the pandemic in Colombia', Communications Medicine, vol. 3, no. 1, 97. https://doi.org/10.1038/s43856-023-00328-3

TY - JOUR

T1 - Genomic epidemiology of SARS-CoV-2 variants during the first two years of the pandemic in Colombia

AU - Jimenez-Silva, Cinthy

AU - Rivero, Ricardo

AU - Douglas, Jordan

AU - Bouckaert, Remco

AU - Villabona-Arenas, Ch. Julian

AU - Atkins, Katherine E.

AU - Gastelbondo, Bertha

AU - Calderon, Alfonso

AU - Guzman, Camilo

AU - Echeverri-De la Hoz, Daniel

AU - Muñoz, Marina

AU - Ballesteros, Nathalia

AU - Castañeda, Sergio

AU - Patiño, Luz H.

AU - Ramirez, Angie

AU - Luna, Nicolas

AU - Paniz-Mondolfi, Alberto

AU - Serrano-Coll, Hector

AU - Ramirez, Juan David

AU - Mattar, Salim

AU - Drummond, Alexei J.

N1 - This work is supported by the Marsden grant 18-UOA-096 from the Royal Society of New Zealand, Colombia’s Science Ministry (Minciencias), BPIN 20200000100090. This project was funded by the Universidad del Rosario in the framework of its strategic plan RUTA2025. Thanks to President and the University Council for leading the strategic projects (JR). We also thank the Colombian network for SARS-CoV-2 genomic surveillance led by the National Institute of Health (INS). C.J.V.-A. and K.E.A. were funded by the European Research Council (ERC) Starting Grant 757688 (to K.E.A.). We thank the National Genomic Surveillance Network of the National Institute of Health (Red de Vigilancia Genómica del Instituto Nacional de Salud) for generating and curating the SARS-COV-2 data that made this study possible.

PY - 2023/7/13

Y1 - 2023/7/13

N2 - The emergence of highly transmissible SARS-CoV-2 variants has led to surges in cases and the need for global genomic surveillance. While some variants rapidly spread worldwide, other variants only persist nationally. There is a need for more fine-scale analysis to understand transmission dynamics at a country scale. For instance, the Mu variant of interest, also known as lineage B.1.621, was first detected in Colombia and was responsible for a large local wave but only a few sporadic cases elsewhere.

AB - The emergence of highly transmissible SARS-CoV-2 variants has led to surges in cases and the need for global genomic surveillance. While some variants rapidly spread worldwide, other variants only persist nationally. There is a need for more fine-scale analysis to understand transmission dynamics at a country scale. For instance, the Mu variant of interest, also known as lineage B.1.621, was first detected in Colombia and was responsible for a large local wave but only a few sporadic cases elsewhere.

U2 - 10.1038/s43856-023-00328-3

DO - 10.1038/s43856-023-00328-3

M3 - Article

SN - 2730-664X

VL - 3

JO - Communications Medicine

JF - Communications Medicine

IS - 1

M1 - 97

ER -

Genomic epidemiology of SARS-CoV-2 variants during the first two years of the pandemic in Colombia

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HIV-1 acquisition and the future of prevention strategies: deciphering the eclipse phase through modelling and phylogenetics - HIV ECLIPSE

Cite this