GrippeCanadaV3, Main, Exploration, bibRecord, 000036

Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014-15.

Identifieur interne : 000036 ( Main/Exploration ); précédent : 000035; suivant : 000037

Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014-15.

Auteurs : Derek R. Macfadden ; Allison Mcgeer ; Taryn Athey ; Stephen Perusini ; Romy Olsha ; Aimin Li ; Alireza Eshaghi ; Jonathan B. Gubbay ; William P. Hanage

Source :

Emerging infectious diseases [ 1080-6059 ] ; 2018.

RBID : pubmed:29460729

Descripteurs français

KwdFr :
- Courbe ROC, Flambées de maladies, Grippe humaine (histoire), Grippe humaine (virologie), Grippe humaine (épidémiologie), Génome viral, Génomique (), Histoire du 21ème siècle, Humains, Ontario, Phylogénie, Saisons, Surveillance de la santé publique, Séquençage nucléotidique à haut débit, Virus de la grippe A (), Virus de la grippe A (génétique), Études rétrospectives.
MESH :
- génétique : Virus de la grippe A.
- histoire : Grippe humaine.
- virologie : Grippe humaine.
- épidémiologie : Grippe humaine.
- Courbe ROC, Flambées de maladies, Génome viral, Génomique, Histoire du 21ème siècle, Humains, Ontario, Phylogénie, Saisons, Surveillance de la santé publique, Séquençage nucléotidique à haut débit, Virus de la grippe A, Études rétrospectives.

English descriptors

KwdEn :
- Disease Outbreaks, Genome, Viral, Genomics (methods), High-Throughput Nucleotide Sequencing, History, 21st Century, Humans, Influenza A virus (classification), Influenza A virus (genetics), Influenza, Human (epidemiology), Influenza, Human (history), Influenza, Human (virology), Ontario, Phylogeny, Public Health Surveillance, ROC Curve, Retrospective Studies, Seasons.
MESH :
- geographic : Ontario.
- classification : Influenza A virus.
- epidemiology : Influenza, Human.
- genetics : Influenza A virus.
- history : Influenza, Human.
- methods : Genomics.
- virology : Influenza, Human.
- Disease Outbreaks, Genome, Viral, High-Throughput Nucleotide Sequencing, History, 21st Century, Humans, Phylogeny, Public Health Surveillance, ROC Curve, Retrospective Studies, Seasons.

Abstract

Adequacy of the current clinical definition of institutional influenza outbreaks is unclear. We performed a retrospective genome sequencing and epidemiologic analysis of institutional influenza outbreaks that occurred during the 2014-15 influenza season in Toronto, Canada. We sequenced the 2 earliest submitted samples positive for influenza A(H3N2) from each of 38 reported institutional outbreaks in long-term care facilities. Genome sequencing showed most outbreak pairs identified by using the current clinical definition were highly related. Inclusion of surveillance samples demonstrated that outbreak sources were likely introductions from broader circulating lineages. Pairwise distance analysis using majority genome and hemagglutinin-specific genes enabled identification of thresholds for discrimination of within and between outbreak pairs; the area under the curve ranged 0.93-0.95. Routine genome sequencing for defining influenza outbreaks in long-term care facilities is unlikely to add significantly to the current clinical definition. Sequencing may prove most useful for investigating sources of outbreak introductions.

DOI: 10.3201/eid2403.171499
PubMed: 29460729

Affiliations:

Links toward previous steps (curation, corpus...)

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Le document en format XML

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<front><div type="abstract" xml:lang="en">Adequacy of the current clinical definition of institutional influenza outbreaks is unclear. We performed a retrospective genome sequencing and epidemiologic analysis of institutional influenza outbreaks that occurred during the 2014-15 influenza season in Toronto, Canada. We sequenced the 2 earliest submitted samples positive for influenza A(H3N2) from each of 38 reported institutional outbreaks in long-term care facilities. Genome sequencing showed most outbreak pairs identified by using the current clinical definition were highly related. Inclusion of surveillance samples demonstrated that outbreak sources were likely introductions from broader circulating lineages. Pairwise distance analysis using majority genome and hemagglutinin-specific genes enabled identification of thresholds for discrimination of within and between outbreak pairs; the area under the curve ranged 0.93-0.95. Routine genome sequencing for defining influenza outbreaks in long-term care facilities is unlikely to add significantly to the current clinical definition. Sequencing may prove most useful for investigating sources of outbreak introductions.</div>
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<name sortKey="Hanage, William P" sort="Hanage, William P" uniqKey="Hanage W" first="William P" last="Hanage">William P. Hanage</name>
<name sortKey="Li, Aimin" sort="Li, Aimin" uniqKey="Li A" first="Aimin" last="Li">Aimin Li</name>
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   |clé=     pubmed:29460729
   |texte=   Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014-15.
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Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014-15.

Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014-15.

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