Journal Article

SARS-CoV-2 Genomic Characteristics and Clinical Impact of SARS-CoV-2 Viral Diversity in Critically Ill COVID-19 Patients: A Prospective Multicenter Cohort Study

Rodriguez, Christophe, Dubois, Claire, Arrestier, Romain, Clere-Jehl, Raphaël, Descamps, Diane, Roque-Afonso, Anne-Marie, Visseaux, Benoit, Brichler, Ségolène, Morand-Joubert, Laurence, Marot, Stéphane, Gaudry, Stéphane, Chaix, Marie-Laure, Voiriot, Guillaume, Roux, Damien, Landraud, Luce, Fourati, Slim, Urbina, Tomas, Ait Hamou, Zakaria, Mayaux, Julien, Luyt, Charles-Edouard, L’honneur, Anne-Sophie, Marcelin, Anne-Geneviève, Pham, Tài, Pawlotsky, Jean-Michel, Bellaiche, Raphael, Salmona, Maud, Audureau, Etienne, Mekontso Dessap, Armand, de Prost, Nicolas, Azoulay, Elie

2022

Overview

The SARS-CoV-2 variant of concern, α, spread worldwide at the beginning of 2021. It was suggested that this variant was associated with a higher risk of mortality than other variants. We aimed to characterize the genetic diversity of SARS-CoV-2 variants isolated from patients with severe COVID-19 and unravel the relationships between specific viral mutations/mutational patterns and clinical outcomes. This is a prospective multicenter observational cohort study. Patients aged ≥18 years admitted to 11 intensive care units (ICUs) in hospitals in the Greater Paris area for SARS-CoV-2 infection and acute respiratory failure between 1 October 2020 and 30 May 2021 were included. The primary clinical endpoint was day-28 mortality. Full-length SARS-CoV-2 genomes were sequenced by means of next-generation sequencing (Illumina COVIDSeq). In total, 413 patients were included, 183 (44.3%) were infected with pre-existing variants, 197 (47.7%) were infected with variant α, and 33 (8.0%) were infected with other variants. The patients infected with pre-existing variants were significantly older (64.9 ± 11.9 vs. 60.5 ± 11.8 years; p = 0.0005) and had more frequent COPD (11.5% vs. 4.1%; p = 0.009) and higher SOFA scores (4 [3–8] vs. 3 [2–4]; 0.0002). The day-28 mortality was no different between the patients infected with pre-existing, α, or other variants (31.1% vs. 26.2% vs. 30.3%; p = 0.550). There was no association between day-28 mortality and specific variants or the presence of specific mutations. At ICU admission, the patients infected with pre-existing variants had a different clinical presentation from those infected with variant α, but mortality did not differ between these groups. There was no association between specific variants or SARS-CoV-2 genome mutational pattern and day-28 mortality.

• Publisher: MDPI AG,MDPI
• Subject: acute respiratory failure / Chronic obstructive pulmonary disease / Clinical outcomes / Cohort analysis / cohort studies / Coronaviruses / COVID-19 / COVID-19 infection / Genetic diversity / genetic variation / genome / Genomes / genomics / Infections / Intensive care / intensive care unit / Intensive care units / Life Sciences / Microbiology and Parasitology / Mortality / Mutation / Next-generation sequencing / Patients / Respiratory failure / risk / SARS-CoV-2 / Severe acute respiratory syndrome coronavirus 2 / variant of concern / Virology