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Vigilancia genómica de variantes del coronavirus del SARS-CoV-2 en pacientes hospitalizados: una cohorte del área metropolitana del valle de Aburrá, Colombia.

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Title: Vigilancia genómica de variantes del coronavirus del SARS-CoV-2 en pacientes hospitalizados: una cohorte del área metropolitana del valle de Aburrá, Colombia.
Alternate Title: Genomic surveillance of SARS-CoV-2 variants in hospitalized patients: a cohort study from the metropolitan area of valle de Aburrá, Colombia.
Authors: Hernández-Ortiz, Olga H.1,2,3 ohelena.hernandez@udea.edu.co, Pérez-Restrepo, Laura1, Úsuga, Jaime1, Moreno, Melissa1, Naranjo, Andrés2, Vélez, Juan4,5, Sará, Jorge6, Molina-Saldarriaga, Francisco7, Jaimes, Fabián3, Osorio, Jorge8, Hernández-Ortiz, Juan P.1,9
Source: Biomédica: Revista del Instituto Nacional de Salud. mar2026, Vol. 46 Issue 1, p48-70. 23p.
Subjects: SARS-CoV-2, CORONAVIRUS spike protein, SARS-CoV-2 Omicron variant, MOLECULAR epidemiology, QUARANTINE, HOSPITAL patients, SARS-CoV-2 Delta variant
Geographic Terms: COLOMBIA
Abstract (English): Introduction. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been one of the most significant pandemics of the modern era. This coronavirus has a high mutation rate, resulting in variants with changes in the spike protein, which hinder containment efforts. Genomic surveillance is crucial for public health and vaccination strategies, especially in low-and middle-income countries, where the impact has been considerable. Objective. To identify viral variants and their clinical presentations in a prospective cohort of hospitalized patients with SARS-CoV-2 infection between October 2021 and February 2023. Materials and methods. We collected patients’ demographic data, medical histories, vaccination status, and clinical progression. Viral genome sequencing was performed on nasopharyngeal swab samples confirmed by real-time reverse transcription polymerase chain reaction to classify strains and detect variants. Results. The predominant variant in the 63 SARS-CoV-2-positive samples was omicron (84%), followed by delta (14%). A higher proportion of critical illness was observed in delta cases (100%) compared to omicron (30%). Mutations in the spike protein were identified and classified into four categories (A-D), along with specific mutations in the S gene. Conclusion. The mutational patterns observed in this study are consistent with global reports, with delta cases presenting greater clinical severity. We identified spike protein mutations that may confer distinctive properties to the virus. These findings underscore the need for ongoing genomic surveillance to better understand viral dynamics and guide public health strategies. [ABSTRACT FROM AUTHOR]
Abstract (Spanish): Introducción. El coronavirus del SARS-CoV-2 ha sido una de las pandemias más significativas de la era moderna. Es un coronavirus con alta tasa de mutación, lo que genera variantes con cambios en la proteína espícula (spike), que dificulta su contención. La vigilancia genómica es crucial para adaptar estrategias de salud pública y vacunación, especialmente en los países de ingresos bajos y medios, donde el impacto ha sido considerable. Objetivo. Identificar variantes virales y sus presentaciones clínicas en una cohorte prospectiva de pacientes hospitalizados con infección por SARS-CoV-2 entre octubre de 2021 y febrero de 2023. Materiales y métodos. Se recopilaron datos demográficos, historial médico, estado de vacunación y progresión clínica. Se hizo secuenciación del genoma viral en muestras de hisopados nasales confirmadas con la prueba de reacción en cadena de la polimerasa en tiempo real con transcripción inversa para clasificar las cepas y detectar variantes. Resultados. De 63 muestras positivas para SARS-CoV-2, la variante predominante fue ómicron (84 %), seguida de la delta (14 %). La variante delta presentó la mayor proporción de enfermedad grave (100 % casos críticos) comparada con ómicron (30 % casos críticos). Se identificaron mutaciones en la proteína espícula en cuatro categorías (A-D), junto con mutaciones específicas del gen S. Conclusión. Los patrones de mutación observados coinciden con los reportes globales, con mayor seriedad clínica en la variante delta. Se identificaron mutaciones en la proteína espiga que confieren propiedades distintivas al virus. Estos hallazgos resaltan la necesidad de la vigilancia genómica continua para comprender la dinámica de la infección y orientar las estrategias de salud pública. [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.)
Database: MedicLatina
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  Data: Vigilancia genómica de variantes del coronavirus del SARS-CoV-2 en pacientes hospitalizados: una cohorte del área metropolitana del valle de Aburrá, Colombia.
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  Data: Genomic surveillance of SARS-CoV-2 variants in hospitalized patients: a cohort study from the metropolitan area of valle de Aburrá, Colombia.
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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>. mar2026, Vol. 46 Issue 1, p48-70. 23p.
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  Data: <searchLink fieldCode="DE" term="%22SARS-CoV-2%22">SARS-CoV-2</searchLink><br /><searchLink fieldCode="DE" term="%22CORONAVIRUS+spike+protein%22">CORONAVIRUS spike protein</searchLink><br /><searchLink fieldCode="DE" term="%22SARS-CoV-2+Omicron+variant%22">SARS-CoV-2 Omicron variant</searchLink><br /><searchLink fieldCode="DE" term="%22MOLECULAR+epidemiology%22">MOLECULAR epidemiology</searchLink><br /><searchLink fieldCode="DE" term="%22QUARANTINE%22">QUARANTINE</searchLink><br /><searchLink fieldCode="DE" term="%22HOSPITAL+patients%22">HOSPITAL patients</searchLink><br /><searchLink fieldCode="DE" term="%22SARS-CoV-2+Delta+variant%22">SARS-CoV-2 Delta variant</searchLink>
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  Label: Abstract (English)
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  Data: Introduction. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been one of the most significant pandemics of the modern era. This coronavirus has a high mutation rate, resulting in variants with changes in the spike protein, which hinder containment efforts. Genomic surveillance is crucial for public health and vaccination strategies, especially in low-and middle-income countries, where the impact has been considerable. Objective. To identify viral variants and their clinical presentations in a prospective cohort of hospitalized patients with SARS-CoV-2 infection between October 2021 and February 2023. Materials and methods. We collected patients’ demographic data, medical histories, vaccination status, and clinical progression. Viral genome sequencing was performed on nasopharyngeal swab samples confirmed by real-time reverse transcription polymerase chain reaction to classify strains and detect variants. Results. The predominant variant in the 63 SARS-CoV-2-positive samples was omicron (84%), followed by delta (14%). A higher proportion of critical illness was observed in delta cases (100%) compared to omicron (30%). Mutations in the spike protein were identified and classified into four categories (A-D), along with specific mutations in the S gene. Conclusion. The mutational patterns observed in this study are consistent with global reports, with delta cases presenting greater clinical severity. We identified spike protein mutations that may confer distinctive properties to the virus. These findings underscore the need for ongoing genomic surveillance to better understand viral dynamics and guide public health strategies. [ABSTRACT FROM AUTHOR]
– Name: Abstract
  Label: Abstract (Spanish)
  Group: Ab
  Data: Introducción. El coronavirus del SARS-CoV-2 ha sido una de las pandemias más significativas de la era moderna. Es un coronavirus con alta tasa de mutación, lo que genera variantes con cambios en la proteína espícula (spike), que dificulta su contención. La vigilancia genómica es crucial para adaptar estrategias de salud pública y vacunación, especialmente en los países de ingresos bajos y medios, donde el impacto ha sido considerable. Objetivo. Identificar variantes virales y sus presentaciones clínicas en una cohorte prospectiva de pacientes hospitalizados con infección por SARS-CoV-2 entre octubre de 2021 y febrero de 2023. Materiales y métodos. Se recopilaron datos demográficos, historial médico, estado de vacunación y progresión clínica. Se hizo secuenciación del genoma viral en muestras de hisopados nasales confirmadas con la prueba de reacción en cadena de la polimerasa en tiempo real con transcripción inversa para clasificar las cepas y detectar variantes. Resultados. De 63 muestras positivas para SARS-CoV-2, la variante predominante fue ómicron (84 %), seguida de la delta (14 %). La variante delta presentó la mayor proporción de enfermedad grave (100 % casos críticos) comparada con ómicron (30 % casos críticos). Se identificaron mutaciones en la proteína espícula en cuatro categorías (A-D), junto con mutaciones específicas del gen S. Conclusión. Los patrones de mutación observados coinciden con los reportes globales, con mayor seriedad clínica en la variante delta. Se identificaron mutaciones en la proteína espiga que confieren propiedades distintivas al virus. Estos hallazgos resaltan la necesidad de la vigilancia genómica continua para comprender la dinámica de la infección y orientar las estrategias de salud pública. [ABSTRACT FROM AUTHOR]
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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.)
PLink https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=lth&AN=192272129
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