Genomic characterization of SARS-CoV-2 and its association with clinical outcomes: a 1-year longitudinal study of the pandemic in Colombia

Ángela María Ruiz-Sternberg, Henry Mauricio Chaparro-Solano, Ludwig L. Albornóz, Ángela María Pinzón-Rondón, Juan Mauricio Pardo-Oviedo, Nicolás Molano-González, Diego Andrés Otero-Rodríguez, Fabio Andrés Zapata-Gómez, Jubby Marcela Gálvez

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Objectives: This study aimed to explore associations between the molecular characterization of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and disease severity in ambulatory and hospitalized patients in two main Colombian epicentres during the first year of the coronavirus disease 2019 pandemic. Methods: In total, 1000 patients with SARS-CoV-2 infection were included in this study. Clinical data were collected from 997 patients, and 678 whole-genome sequences were obtained by massively parallel sequencing. Bivariate, multi-variate, and classification and regression tree analyses were run between clinical and genomic variables. Results: Age >88 years, and infection with lineages B.1.1, B.1.1.388, B.1.523 or B.1.621 for patients aged 71–88 years were associated with death [odds ratio (OR) 6.048036, 95% confidence interval (CI) 1.346567–32.92521; P=0.01718674]. The need for hospitalization was associated with higher age and comorbidities. The hospitalization rate increased significantly for patients aged 38–51 years infected with lineages A, B, B.1.1.388, B.1.1.434, B.1.153, B.1.36.10, B.1.411, B.1.471, B.1.558 or B.1.621 (OR 8.368427, 95% CI 2.573145–39.10672, P=0.00012). Associations between clades and clinical outcomes diverged from previously reported data. Conclusions: Infection with lineage B.1.621 increased the hospitalization and mortality rates. These findings, plus the rapidly increasing prevalence in Colombia and other countries, suggest that lineage B.1.621 should be considered as a ‘variant of interest’. If associated disease severity is confirmed, possible designation as a ‘variant of concern’ should be considered.

Original languageEnglish (US)
Pages (from-to)91-100
Number of pages10
JournalInternational Journal of Infectious Diseases
Early online dateDec 15 2021
StatePublished - Mar 2022

All Science Journal Classification (ASJC) codes

  • Microbiology (medical)
  • Infectious Diseases


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