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

https://doi.org/10.1016/j.ijid.2021.12.326Get rights and content
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Highlights

  • Lineages B.1.621 and B.1.1.388 are associated with higher hospitalization and mortality rates.

  • Lineage B.1.621 was first detected in September 2020 worldwide.

  • Lineage B.1.621 became predominant in Colombia during the most serious outbreak.

  • Associations between clades and clinical outcomes found in this study diverged from previous reported data.

ABSTRACT

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.

Keywords

SARS-CoV-2
SARS-CoV-2 variants
COVID-19
Mortality
Hospitalization
High-throughput nucleotide sequencing

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