Patient health records and whole viral genomes from an early SARS-CoV-2 outbreak in a Quebec hospital reveal features associated with favorable outcomes.
PLoS One
; 16(12): e0260714, 2021.
Artículo
en Inglés
| MEDLINE | ID: covidwho-1546965
ABSTRACT
The first confirmed case of COVID-19 in Quebec, Canada, occurred at Verdun Hospital on February 25, 2020. A month later, a localized outbreak was observed at this hospital. We performed tiled amplicon whole genome nanopore sequencing on nasopharyngeal swabs from all SARS-CoV-2 positive samples from 31 March to 17 April 2020 in 2 local hospitals to assess viral diversity (unknown at the time in Quebec) and potential associations with clinical outcomes. We report 264 viral genomes from 242 individuals-both staff and patients-with associated clinical features and outcomes, as well as longitudinal samples and technical replicates. Viral lineage assessment identified multiple subclades in both hospitals, with a predominant subclade in the Verdun outbreak, indicative of hospital-acquired transmission. Dimensionality reduction identified two subclades with mutations of clinical interest, namely in the Spike protein, that evaded supervised lineage assignment methods-including Pangolin and NextClade supervised lineage assignment tools. We also report that certain symptoms (headache, myalgia and sore throat) are significantly associated with favorable patient outcomes. Our findings demonstrate the strength of unsupervised, data-driven analyses whilst suggesting that caution should be used when employing supervised genomic workflows, particularly during the early stages of a pandemic.
Texto completo:
Disponible
Colección:
Bases de datos internacionales
Base de datos:
MEDLINE
Asunto principal:
Infección Hospitalaria
/
Brotes de Enfermedades
/
Genoma Viral
/
SARS-CoV-2
/
COVID-19
Tipo de estudio:
Estudio observacional
/
Estudio pronóstico
/
Ensayo controlado aleatorizado
Límite:
Adolescente
/
Adulto
/
Anciano
/
Niño
/
Child, preschool
/
Femenino
/
Humanos
/
Masculino
/
Middle aged
/
Young_adult
País/Región como asunto:
America del Norte
Idioma:
Inglés
Revista:
PLoS One
Asunto de la revista:
Ciencia
/
Medicina
Año:
2021
Tipo del documento:
Artículo
País de afiliación:
Journal.pone.0260714
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