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Caracterización de genomas recombinantes de la variante ómicron del SARS-CoV-2 entre el 2022 y el 2023 en el departamento de Antioquia, Colombia.

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Title: Caracterización de genomas recombinantes de la variante ómicron del SARS-CoV-2 entre el 2022 y el 2023 en el departamento de Antioquia, Colombia.
Alternate Title: Characterization of recombinant genomes of the omicron variant of SARS-CoV-2 between 2022 and 2023 in the department of Antioquia, Colombia.
Authors: Velarde, Cristian Arbey1, Vega, Leila Cristina1, Betancur, Idabely1 idabely.betancur@antioquia.gov.co
Source: Biomédica: Revista del Instituto Nacional de Salud. jun2026, Vol. 46 Issue 2, p228-245. 18p.
Subjects: SARS-CoV-2 Omicron variant, RECOMBINANT viruses, PHYLOGENY, VIRUS diseases, AMINO acid sequence, NUCLEOTIDE sequencing, SARS-CoV-2
Geographic Terms: ANTIOQUIA (Colombia : Dept.), COLOMBIA
Abstract (English): Introduction. Recombination is a mechanism that prevents the accumulation of noxious mutations. Recombination occurs between different sublineages of the same virus that are co-circulating and co-infecting the same host. Next-generation sequencing technologies have allowed the identification of recombinant sublineages of omicron. Objective. To describe how viral recombination in new omicron lineages has conferred important characteristics to this variant and allowed its prevalence. Materials and methods. A total of 338 genomes of recombinant lineages from positive samples of SARS-CoV-2 analyzed by the Laboratorio Departamental de Salud Pública de Antioquia were characterized, between November 9, 2022, and November 5, 2023. The genomes were obtained using Oxford Nanopore™ sequencing technology. Phylogenetic analysis identified different recombinant sublineages of omicron and predictors allowed the identification of regions in the SARS-CoV-2 genome that were the product of recombination events. Results. Twenty-six recombinant lineages of omicron were identified, and important amino acid changes were found involved in evasion of the immune response, infectivity and increased viral replication, N501Y, D614G and P681H. The F456L variant was also identified and was present in 55% of the XBB.1.5.72 genomes and is a biomarker for recognition of this sublineage. The analysis with recombination predictors allowed the identification of the potential parents of some recombinant genomes such as XBB.1.5 and XBB.1.5.77. Conclusion. The circulation of omicron sublineage recombinants shows important changes that impact their biology and have altered infection and virulence factors. [ABSTRACT FROM AUTHOR]
Abstract (Spanish): Introducción. La recombinación es un mecanismo que evita la acumulación de mutaciones nocivas. Para que se dé entre diferentes sublinajes de un mismo virus, se requiere cocirculación y coinfección en un mismo huésped. Mediante NGS (next-generation sequencing) se han podido caracterizar linajes recombinantes de la variante ómicron. Objetivo. Describir cómo la recombinación viral en linajes de ómicron le ha conferido características importantes para su prevalencia sobre otros linajes. Materiales y métodos. Se caracterizaron 338 genomas de linajes recombinantes de muestras positivas de SARS-CoV-2 analizadas por el Laboratorio Departamental de Salud Pública de Antioquia, entre el 9 de noviembre del 2022 y el 5 de noviembre del 2023. Los genomas fueron obtenidos mediante la tecnología de secuenciación de Oxford Nanopore™. Por medio de análisis filogenéticos se identificaron diferentes sublinajes recombinantes de ómicron. Predictores permitieron la identificación de regiones del genoma de SARS-CoV-2 que habían sido producto de eventos de recombinación. Resultados. Se identificaron 26 linajes recombinantes de ómicron en los que se encontraron cambios de aminoácidos de gran importancia, involucrados en la evasión de la respuesta inmunitaria, infectividad y replicación viral. También se identificó la mutación F456L, presente en el 55 % de los genomas de XBB.1.5.72, que sirve como biomarcador de reconocimiento de este sublinaje. Los análisis con predictores permitieron la identificación de los probables linajes parentales de algunos genomas recombinantes como XBB.1.5 y XBB.1.5.77. Conclusión. La circulación de sublinajes recombinantes de ómicron muestran cambios importantes que impactan la biología de estos y han alterado los factores de infección y virulencia. [ABSTRACT FROM AUTHOR]
Copyright of Biomédica: Revista del Instituto Nacional de Salud is the property of Instituto Nacional de Salud of Colombia and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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  Data: Caracterización de genomas recombinantes de la variante ómicron del SARS-CoV-2 entre el 2022 y el 2023 en el departamento de Antioquia, Colombia.
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  Data: Characterization of recombinant genomes of the omicron variant of SARS-CoV-2 between 2022 and 2023 in the department of Antioquia, Colombia.
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  Data: <searchLink fieldCode="AR" term="%22Velarde%2C+Cristian+Arbey%22">Velarde, Cristian Arbey</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Vega%2C+Leila+Cristina%22">Vega, Leila Cristina</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Betancur%2C+Idabely%22">Betancur, Idabely</searchLink><relatesTo>1</relatesTo><i> idabely.betancur@antioquia.gov.co</i>
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  Data: <searchLink fieldCode="JN" term="%22Biomédica%3A+Revista+del+Instituto+Nacional+de+Salud%22">Biomédica: Revista del Instituto Nacional de Salud</searchLink>. jun2026, Vol. 46 Issue 2, p228-245. 18p.
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  Data: <searchLink fieldCode="DE" term="%22SARS-CoV-2+Omicron+variant%22">SARS-CoV-2 Omicron variant</searchLink><br /><searchLink fieldCode="DE" term="%22RECOMBINANT+viruses%22">RECOMBINANT viruses</searchLink><br /><searchLink fieldCode="DE" term="%22PHYLOGENY%22">PHYLOGENY</searchLink><br /><searchLink fieldCode="DE" term="%22VIRUS+diseases%22">VIRUS diseases</searchLink><br /><searchLink fieldCode="DE" term="%22AMINO+acid+sequence%22">AMINO acid sequence</searchLink><br /><searchLink fieldCode="DE" term="%22NUCLEOTIDE+sequencing%22">NUCLEOTIDE sequencing</searchLink><br /><searchLink fieldCode="DE" term="%22SARS-CoV-2%22">SARS-CoV-2</searchLink>
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  Data: <searchLink fieldCode="DE" term="%22ANTIOQUIA+%28Colombia+%3A+Dept%2E%29%22">ANTIOQUIA (Colombia : Dept.)</searchLink><br /><searchLink fieldCode="DE" term="%22COLOMBIA%22">COLOMBIA</searchLink>
– Name: Abstract
  Label: Abstract (English)
  Group: Ab
  Data: Introduction. Recombination is a mechanism that prevents the accumulation of noxious mutations. Recombination occurs between different sublineages of the same virus that are co-circulating and co-infecting the same host. Next-generation sequencing technologies have allowed the identification of recombinant sublineages of omicron. Objective. To describe how viral recombination in new omicron lineages has conferred important characteristics to this variant and allowed its prevalence. Materials and methods. A total of 338 genomes of recombinant lineages from positive samples of SARS-CoV-2 analyzed by the Laboratorio Departamental de Salud Pública de Antioquia were characterized, between November 9, 2022, and November 5, 2023. The genomes were obtained using Oxford Nanopore™ sequencing technology. Phylogenetic analysis identified different recombinant sublineages of omicron and predictors allowed the identification of regions in the SARS-CoV-2 genome that were the product of recombination events. Results. Twenty-six recombinant lineages of omicron were identified, and important amino acid changes were found involved in evasion of the immune response, infectivity and increased viral replication, N501Y, D614G and P681H. The F456L variant was also identified and was present in 55% of the XBB.1.5.72 genomes and is a biomarker for recognition of this sublineage. The analysis with recombination predictors allowed the identification of the potential parents of some recombinant genomes such as XBB.1.5 and XBB.1.5.77. Conclusion. The circulation of omicron sublineage recombinants shows important changes that impact their biology and have altered infection and virulence factors. [ABSTRACT FROM AUTHOR]
– Name: Abstract
  Label: Abstract (Spanish)
  Group: Ab
  Data: Introducción. La recombinación es un mecanismo que evita la acumulación de mutaciones nocivas. Para que se dé entre diferentes sublinajes de un mismo virus, se requiere cocirculación y coinfección en un mismo huésped. Mediante NGS (next-generation sequencing) se han podido caracterizar linajes recombinantes de la variante ómicron. Objetivo. Describir cómo la recombinación viral en linajes de ómicron le ha conferido características importantes para su prevalencia sobre otros linajes. Materiales y métodos. Se caracterizaron 338 genomas de linajes recombinantes de muestras positivas de SARS-CoV-2 analizadas por el Laboratorio Departamental de Salud Pública de Antioquia, entre el 9 de noviembre del 2022 y el 5 de noviembre del 2023. Los genomas fueron obtenidos mediante la tecnología de secuenciación de Oxford Nanopore™. Por medio de análisis filogenéticos se identificaron diferentes sublinajes recombinantes de ómicron. Predictores permitieron la identificación de regiones del genoma de SARS-CoV-2 que habían sido producto de eventos de recombinación. Resultados. Se identificaron 26 linajes recombinantes de ómicron en los que se encontraron cambios de aminoácidos de gran importancia, involucrados en la evasión de la respuesta inmunitaria, infectividad y replicación viral. También se identificó la mutación F456L, presente en el 55 % de los genomas de XBB.1.5.72, que sirve como biomarcador de reconocimiento de este sublinaje. Los análisis con predictores permitieron la identificación de los probables linajes parentales de algunos genomas recombinantes como XBB.1.5 y XBB.1.5.77. Conclusión. La circulación de sublinajes recombinantes de ómicron muestran cambios importantes que impactan la biología de estos y han alterado los factores de infección y virulencia. [ABSTRACT FROM AUTHOR]
– Name: AbstractSuppliedCopyright
  Label:
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  Data: <i>Copyright of Biomédica: Revista del Instituto Nacional de Salud is the property of Instituto Nacional de Salud of Colombia and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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              Text: jun2026
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