TY - JOUR
T1 - Genomic characterization of SARS-CoV-2 and its association with clinical outcomes
T2 - a 1-year longitudinal study of the pandemic in Colombia
AU - Ruiz-Sternberg, Ángela María
AU - Chaparro-Solano, Henry Mauricio
AU - Albornóz, Ludwig L.
AU - Pinzón-Rondón, Ángela María
AU - Pardo-Oviedo, Juan Mauricio
AU - Molano-González, Nicolás
AU - Otero-Rodríguez, Diego Andrés
AU - Zapata-Gómez, Fabio Andrés
AU - Gálvez, Jubby Marcela
N1 - Funding Information:
The authors wish to thank Lina Marcela Méndez Castillo, Andrés Felipe Torres Gómez and Danyela Faisury Valero Rubio for supporting the laboratory procedures; and Andrea del Pilar Hernández Rodríguez, Andrés Felipe Patiño Aldana, Liseth Belinda Cifuentes Saenz, Natalia Andrea Pedraza López, Mateo Andrés Díaz Quiroz, Kevin Daniel Rivera Mendoza, Isabella Caicedo, María Alejandra Urbano, Alejandra Hidalgo and all other members of the Clinical Investigation Group that supported the collection of clinical data and development of this research. This work was supported by governmental funding from the Colombian Ministry of Science, Technology and Innovation (Grant No. 366-2020). This study was approved by the institutional review boards of Universidad del Rosario and participating hospital research centres. All international and national bioethical principles and regulations for clinical investigation in human subjects were followed.
Funding Information:
This work was supported by governmental funding from the Colombian Ministry of Science, Technology and Innovation (Grant No. 366-2020).
Publisher Copyright:
© 2021 The Authors
PY - 2022/3
Y1 - 2022/3
N2 - 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.
AB - 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.
KW - COVID-19
KW - High-throughput nucleotide sequencing
KW - Hospitalization
KW - Mortality
KW - SARS-CoV-2
KW - SARS-CoV-2 variants
UR - http://www.scopus.com/inward/record.url?scp=85122807980&partnerID=8YFLogxK
U2 - 10.1016/j.ijid.2021.12.326
DO - 10.1016/j.ijid.2021.12.326
M3 - Artículo
C2 - 34920122
AN - SCOPUS:85122807980
SN - 1201-9712
VL - 116
SP - 91
EP - 100
JO - International Journal of Infectious Diseases
JF - International Journal of Infectious Diseases
ER -