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

Abstract

Objectives This study aims to explore the association between the molecular characterization of SARS-CoV-2 and disease severity on ambulatory and hospitalized patients in two main Colombian epicenters during the first year of the COVID-19 pandemic. Methods We included 1000 patients with SARS-CoV-2 infection, collected clinical data from 997, and obtained 678 whole genome sequences by massively parallel sequencing. Bivariate, multivariate, and classification and regression tree analyses were run between clinical and genomic variables. Results Age and infection with lineages B.1.1, B.1.1.388, B.1.523, and B.1.621 were related to lethality for patients 71-88 years old (OR: 6.048036; 95% CI 1.346567-32.92521, p-value: 0.01718674). The need for hospitalization was associated with higher age and comorbidities. For patients 38-51 years old 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, hospitalization rate increased significantly (OR 8.368427, 95% CI 2.573145-39.10672, p-value: 0.00012). Associations between clades and clinical outcomes diverged from previously reported data. Conclusions Lineage B.1.621 increased the need for hospitalization and lethality. Our findings, plus the rapidly increasing prevalence in Colombia and other countries, suggest broadly considering it as a Variant of Interest. If associated disease severity is confirmed, possible designation as Variant of Concern could be entertained.

Associated factors for mortality in a COVID-19 colombian cohort: is the third wave relevant when Mu variant was predominant epidemiologically?

“…Moreover, despite previous evidence suggesting an increased risk of hospitalization and mortality in patients with the Mu variant [ 7 ], we did not find an increased hazard in in-hospital mortality during the third epidemic wave in which the Mu variant was predominant in Colombia, probably explained by the protective effect of vaccination surpassing the potential effect of immune evasion of the Mu variant.…”

“…The B.1.621 or Mu variant was first described in Colombia in January 2021 and then considered a Variant of interest (VOI) in August 2021; however, it had been isolated from several samples taken since late 2020, which confirms its circulation since the second Colombian epidemic wave and its predominance in the third epidemic wave [ 4 , 7 ]. It was quickly identified in more than 20 countries, mainly in the Americas [ 8 ].…”

Molecular Epidemiology of SARS-CoV-2 during Five COVID-19 Waves and the Significance of Low-Frequency Lineages

“…In Peru, B.1.1 was detected at a frequency of 1%, while in Chile, it was reported as one of five lineages that dominated early in the pandemic [ 30 , 31 ]. B.1.1.348 was detected in Argentina during the first wave of SARS-CoV-2 infections at a low frequency of 3.7% and was present in Peru at 3% and at a higher frequency of 9.7% in Colombia [ 30 , 32 , 33 ]. Chile also reported B.1.1.348 as one of five dominant lineages early in the pandemic [ 31 ].…”

Retrospective analysis of 261 autopsies of penetrating cardiac injuries with emphasis on sociodemographic factors

“…In order to explore more deeply the factors associated with place at death, we use Classification and Regression Trees 48 as implemented in Rpart R package 49 as an exploratory tool to uncover complex interactions between selected covariates and the place at death. This method has been used before successfully by one of the authors to explore associations on outcomes of interest in the context of observational studies (see for example 50 – 52 ).…”