Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics

PLoS Pathogens
Nicola F MüllerTanja Stadler

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 elde...Continue Reading

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Citations

Mar 24, 2021·Nature Reviews. Microbiology·Nancy H L Leung
May 5, 2021·Science Translational Medicine·Nicola F MüllerTrevor Bedford
May 20, 2021·Molecular Biology and Evolution·Stilianos LoucaMatthew W Pennell

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Datasets Mentioned

BETA
MN299375-MN304713

Software Mentioned

muscle
BEAST2
Beast
BDSKY
bowtie
lofreq
RaxML

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