UFK9FWNK
type: UserItem
resource: Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics
tagged: UserTag
  label: *Disease Outbreaks
tagged: UserTag
  label: *Epidemics
tagged: UserTag
  label: Adolescent
tagged: UserTag
  label: Child
tagged: UserTag
  label: Child, Preschool
tagged: UserTag
  label: Cities
tagged: UserTag
  label: Humans
tagged: UserTag
  label: Influenza A Virus, H3N2 Subtype/*genetics/isolation & purification
tagged: UserTag
  label: Influenza, Human/*epidemiology/transmission/virology
tagged: UserTag
  label: Phylogeny
tagged: UserTag
  label: Seasons
tagged: UserTag
  label: Switzerland/epidemiology

Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics
type: AcademicArticle
abstract: Infecting large portions of the global population, seasonal influenza is a major burden on societies around the globe. While the global source sink dynamics of the different seasonal influenza viruses have been studied intensively, its local spread remains less clear. In order to improve our understanding of how influenza is transmitted on a city scale, we collected an extremely densely sampled set of influenza sequences alongside patient metadata. To do so, we sequenced influenza viruses isolated from patients of two different hospitals, as well as private practitioners in Basel, Switzerland during the 2016/2017 influenza season. The genetic sequences reveal that repeated introductions into the city drove the influenza season. We then reconstruct how the effective reproduction number changed over the course of the season. While we did not find that transmission dynamics in Basel correlate with humidity or school closures, we did find some evidence that it may positively correlated with temperature. Alongside the genetic sequence data that allows us to see how individual cases are connected, we gathered patient information, such as the age or household status. Zooming into the local transmission outbreaks suggests that the elderly were to a large extent infected within their own transmission network. In the remaining transmission network, our analyses suggest that school-aged children likely play a more central role than pre-school aged children. These patterns will be valuable to plan interventions combating the spread of respiratory diseases within cities given that similar patterns are observed for other influenza seasons and cities.
pages: e1008984
doi: 10.1371/journal.ppat.1008984
source: 33211775
creator: Person
author list: Person
is part of: Issue
  date: 2020-11-20
  volume: 16
  issue: 11
  is part of: PLoS Pathog
    type: Journal
    issn: 1553-7374 (Electronic) 1553-7366 (Print) 1553-7366 (Linking)

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given name: N. F.
surname: Muller

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given name: D.
surname: Wuthrich

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given name: N.
surname: Goldman

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surname: Sailer

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surname: Saalfrank

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surname: Brunner

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surname: Augustin

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surname: Seth-Smith

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surname: Hollenstein

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surname: Neher

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surname: Naegele

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surname: Buser

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given name: C. H.
surname: Nickel

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surname: Ritz

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surname: Zeller

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given name: B. M.
surname: Lang

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surname: Bedford

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given name: M.
surname: Battegay

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given name: R.
surname: Schneider-Sliwa

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given name: A.
surname: Egli

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given name: T.
surname: Stadler