Portrait of Léa Kaufmann

Léa Kaufmann

Master's Research - Université de Montréal
Supervisor
Sébastien Lemieux
Research Topics
AI and Healthcare
Website
GitHub

Publications

Patient health records and whole viral genomes from an early SARS-CoV-2 outbreak in a Quebec hospital reveal features associated with favorable outcomes
Bastien Paré
Marieke Rozendaal
Sacha Morin
Raphaël Poujol
Fatima Mostefai
Shawn M. Simpson
Jean-Christophe Grenier
Léa Kaufmann
Henry Xing
Miguelle Sanchez
Ariane Yechouron
Ronald Racette
Julie G. Hussin
Guy Wolf
Ivan Pavlov
Martin A. Smith
The first confirmed case of COVID-19 in Quebec, Canada, occurred at Verdun Hospital on February 25, 2020. A month later, a localized outbrea… (see more)k 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 the viral diversity of the outbreak. We report 264 viral genomes from 242 individuals (both staff and patients) with associated clinical features and outcomes, as well as longitudinal samples, technical replicates and the first publicly disseminated SARS-CoV-2 genomes in Quebec. 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 that evaded supervised lineage assignment methods, including Pangolin, and identified certain symptoms (headache, myalgia and sore throat) that are significantly associated with favorable patient outcomes. We also address certain limitations of standard SARS-CoV-2 bioinformatics procedures, notably when presented with multiple viral haplotypes.
2021-12-01
PLOS ONE (published)
doi.org