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1.
PLoS One ; 16(12): e0260714, 2021.
Article in English | MEDLINE | ID: mdl-34855869

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.


Subject(s)
COVID-19/virology , Cross Infection/virology , Disease Outbreaks , Genome, Viral/genetics , SARS-CoV-2/genetics , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/epidemiology , COVID-19/mortality , Child , Child, Preschool , Cross Infection/epidemiology , Disease Outbreaks/statistics & numerical data , Female , Haplotypes/genetics , Humans , Male , Middle Aged , Phylogeny , Quebec/epidemiology , SARS-CoV-2/pathogenicity , Sequence Analysis, RNA , Treatment Outcome , Young Adult
2.
medRxiv ; 2021 Jun 01.
Article in English | MEDLINE | ID: mdl-34100030

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 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.

3.
PLoS One ; 13(5): e0197509, 2018.
Article in English | MEDLINE | ID: mdl-29795633

ABSTRACT

We consider a multi-agent model of a simple economical system and study the impacts of a wave of immigrants on the stability of the system. Our model couples a labor market with a goods market. We first create a stable economy with N agents and study the impact of adding n new workers in the system. The time to reach a new equilibrium market is found to obey a power law in n. The new wages and market prices are observed to decrease as 1/n, whereas the wealth of agents remains unchanged.


Subject(s)
Emigrants and Immigrants , Emigration and Immigration , Models, Econometric , Algorithms , Humans
4.
Emerg Infect Dis ; 14(9): 1437-9, 2008 Sep.
Article in English | MEDLINE | ID: mdl-18760014

ABSTRACT

The database of a major microbiology laboratory in Israel was searched to determine the prevalence of nontuberculous mycobacterial lymphadenitis in immunocompetent children. We observed a 4-fold increase in nontuberculous mycobacteria isolates during 1985-2006, which was attributable mainly to increased detection of Mycobacterium haemophilum starting in 1996.


Subject(s)
Lymphadenitis/epidemiology , Lymphadenitis/microbiology , Mycobacterium Infections/epidemiology , Mycobacterium haemophilum/isolation & purification , Adolescent , Child , Child, Preschool , Female , Humans , Immunocompetence , Infant , Israel/epidemiology , Male , Mycobacterium avium Complex/isolation & purification
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