Open AccessPatient health records and whole viral genomes from an early SARS-CoV-2 outbreak in a Quebec hospital reveal features associated with favorable outcomes
Author(s) -
Bastien Paré,
Marieke Rozendaal,
Sacha Morin,
Léa Kaufmann,
Shawn M. Simpson,
Raphaël Poujol,
Fatima Mostefai,
Jean Grenier,
Henry Xing,
Miguelle Sanchez,
Ariane Yechouron,
Ronald Racette,
Julie Hussin,
Guy Wolf,
Ivan Petrovitch Pavlov,
Martin A. Smith
Publication year - 2021
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0260714
Subject(s) - outbreak , lineage (genetic) , pangolin , medicine , transmission (telecommunications) , genome , pandemic , biology , virology , genetics , covid-19 , disease , infectious disease (medical specialty) , gene , electrical engineering , engineering , traditional medicine
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.