Dataset Information

GENOMIC CHARACTERIZATION OF SARS-CoV-2 AND ITS ASSOCIATION WITH CLINICAL OUTCOMES: A ONE-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.

SUBMITTER: Ruiz-Sternberg AM

PROVIDER: S-EPMC8673727 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:The coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has shown a wide spectrum of clinical manifestations ranging from asymptomatic infections to severe disease and death. Pre-existing medical conditions and age have been mainly linked to the development of severe disease; however, the potential association of viral genetic characteristics with different clinical conditions remains unclear. SARS-CoV-2 variants with increased transmissibility were detected early in the pandemics, and several variants with potential relevance for public health are currently circulating around the world. In this study, we characterized 57 complete SARS-CoV-2 genomes during the exponential growth phase of the early epidemiological curve in Mexico, in April 2020. Patients were categorized under distinct disease severity outcomes: mild disease or ambulatory care, severe disease or hospitalized, and deceased. To reduce bias related to risk factors, the patients were less than 60 years old and with no diagnosed comorbidities A trait-association phylogenomic approach was used to explore genotype-phenotype associations, represented by the co-occurrence of mutations, disease severity outcome categories, and clusters of Mexican sequences. Phylogenetic results revealed a higher genomic diversity compared to the initial viruses detected during the early stage of the local epidemic. We identified a total of 90 single nucleotide variants compared to the Wuhan-Hu-1 genome, including 54 nonsynonymous mutations. We did not find evidence for the co-occurrence of mutations associated with specific disease outcomes. Therefore, in the group of patients studied, disease severity was likely mainly driven by the host genetic background and other demographic factors. IMPORTANCE The genetic association of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) with different clinical conditions remains unclear and needs further investigation. In this study, we characterized 57 complete SARS-CoV-2 genomes from patients in Mexico with distinct disease severity outcomes: mild disease or ambulatory care, severe disease or hospitalized, and deceased. To reduce bias related to risk factors the patients were less than 60 years old and with no diagnosed comorbidities. We did not find evidence for the co-occurrence of mutations associated with specific disease outcomes. Therefore, in the group of patients studied, disease severity was likely mainly driven by the host genetic background and other demographic factors.