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. 2021 Dec 2;16(12):e0260714. doi: 10.1371/journal.pone.0260714. eCollection 2021.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Aged, 80 and over
  • COVID-19 / epidemiology
  • COVID-19 / mortality
  • COVID-19 / virology*
  • Child
  • Child, Preschool
  • Cross Infection / epidemiology
  • Cross Infection / virology*
  • Disease Outbreaks* / statistics & numerical data
  • Female
  • Genome, Viral / genetics*
  • Haplotypes / genetics
  • Humans
  • Male
  • Middle Aged
  • Phylogeny
  • Quebec / epidemiology
  • SARS-CoV-2 / genetics*
  • SARS-CoV-2 / pathogenicity
  • Sequence Analysis, RNA
  • Treatment Outcome
  • Young Adult

Grant support

SM is supported by an IVADO MSc excellence scholarship and an FRQNT B1X scholarship. JGH is a Fonds de Reherche du Québec en Santé Research Scholar (252997) funded by IVADO COVID19 Rapid Response grant (CVD19-030) and the Montreal Heart Institute Foundation. GW is supported by Canada CIFAR AI Chair. MAS is supported by a Fonds de Reherche du Québec en Santé Junior 1 fellowship (295760).