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High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters

Adrian Egli, Nina Goldman, Nicola F. Müller, Myrta Brunner, Daniel Wüthrich, Sarah Tschudin-Sutter, Emma Hodcroft, View ORCID ProfileRichard Neher, Claudia Saalfrank, James Hadfield, Trevor Bedford, Mohammedyaseen Syedbasha, Thomas Vogel, Noémie Augustin, Jan Bauer, Nadine Sailer, Nadezhda Amar-Sliwa, Daniela Lang, Helena M.B. Seth-Smith, Annette Blaich, Yvonne Hollenstein, Olivier Dubuis, Michael Nägele, Andreas Buser, Christian H. Nickel, Nicole Ritz, Andreas Zeller, Tanja Stadler, Manuel Battegay, Rita Schneider-Sliwa
doi: https://doi.org/10.1101/2020.04.03.023135
Adrian Egli
aClinical Microbiology, University Hospital Basel & University of Basel, Basel, Switzerland
bApplied Microbiology Research, University of Basel, Basel, Switzerland
cDepartment Clinical Research, University of Basel, Basel, Switzerland
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  • For correspondence: adrian.egli@usb.ch
Nina Goldman
dHuman Geography, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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Nicola F. Müller
eDepartment of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
fSwiss Institute of Bioinformatics (SIB), Basel, Switzerland
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Myrta Brunner
dHuman Geography, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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Daniel Wüthrich
aClinical Microbiology, University Hospital Basel & University of Basel, Basel, Switzerland
bApplied Microbiology Research, University of Basel, Basel, Switzerland
fSwiss Institute of Bioinformatics (SIB), Basel, Switzerland
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Sarah Tschudin-Sutter
gInfectious Diseases and Hospital Epidemiology, University Hospital Basel & University of Basel, Basel, Switzerland
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Emma Hodcroft
fSwiss Institute of Bioinformatics (SIB), Basel, Switzerland
hBiozentrum, University of Basel, Basel, Switzerland
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Richard Neher
fSwiss Institute of Bioinformatics (SIB), Basel, Switzerland
hBiozentrum, University of Basel, Basel, Switzerland
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  • ORCID record for Richard Neher
Claudia Saalfrank
dHuman Geography, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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James Hadfield
iFred Hutchinson Cancer Research Center, Seattle, USA
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Trevor Bedford
iFred Hutchinson Cancer Research Center, Seattle, USA
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Mohammedyaseen Syedbasha
bApplied Microbiology Research, University of Basel, Basel, Switzerland
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Thomas Vogel
dHuman Geography, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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Noémie Augustin
dHuman Geography, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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Jan Bauer
dHuman Geography, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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Nadine Sailer
dHuman Geography, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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Nadezhda Amar-Sliwa
dHuman Geography, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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Daniela Lang
aClinical Microbiology, University Hospital Basel & University of Basel, Basel, Switzerland
bApplied Microbiology Research, University of Basel, Basel, Switzerland
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Helena M.B. Seth-Smith
aClinical Microbiology, University Hospital Basel & University of Basel, Basel, Switzerland
bApplied Microbiology Research, University of Basel, Basel, Switzerland
fSwiss Institute of Bioinformatics (SIB), Basel, Switzerland
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Annette Blaich
aClinical Microbiology, University Hospital Basel & University of Basel, Basel, Switzerland
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Yvonne Hollenstein
aClinical Microbiology, University Hospital Basel & University of Basel, Basel, Switzerland
bApplied Microbiology Research, University of Basel, Basel, Switzerland
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Olivier Dubuis
jViollier AG, Allschwil, Switzerland
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Michael Nägele
jViollier AG, Allschwil, Switzerland
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Andreas Buser
kBlood Donation Center, Swiss Red Cross, Basel, Switzerland
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Christian H. Nickel
lEmergency Department, University Hospital Basel, Basel, Switzerland
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Nicole Ritz
mPediatric Infectious Diseases and Vaccinology, University Children’s Hospital Basel and University of Basel, Basel Switzerland
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Andreas Zeller
nCentre for Primary Health Care, University of Basel, Basel, Switzerland
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Tanja Stadler
eDepartment of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
fSwiss Institute of Bioinformatics (SIB), Basel, Switzerland
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Manuel Battegay
gInfectious Diseases and Hospital Epidemiology, University Hospital Basel & University of Basel, Basel, Switzerland
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Rita Schneider-Sliwa
dHuman Geography, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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Abstract

With two-thirds of the global population projected to be living in urban areas by 2050, understanding the transmission patterns of viral pathogens within cities is crucial for effective prevention strategies. Here, in unprecedented spatial resolution, we analysed the socioeconomic determinants of influenza transmission in a European city. We combined geographical and epidemiological data with whole genome sequencing of influenza viruses at the scale of urban quarters and statistical blocks, the smallest geographic subdivisions within a city. We observed annually re-occurring geographic clusters of influenza incidences, mainly associated with net income, and independent of population density and living space. Vaccination against influenza was also mainly associated with household income and was linked to the likelihood of influenza-like illness within an urban quarter. Transmissions patterns within and between quarters were complex. High-resolution city-level epidemiological studies combined with social science surveys such as this will be essential for understanding seasonal and pandemic transmission chains and delivering tailored public health information and vaccination programs at the municipal level.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted April 04, 2020.
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High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters
Adrian Egli, Nina Goldman, Nicola F. Müller, Myrta Brunner, Daniel Wüthrich, Sarah Tschudin-Sutter, Emma Hodcroft, Richard Neher, Claudia Saalfrank, James Hadfield, Trevor Bedford, Mohammedyaseen Syedbasha, Thomas Vogel, Noémie Augustin, Jan Bauer, Nadine Sailer, Nadezhda Amar-Sliwa, Daniela Lang, Helena M.B. Seth-Smith, Annette Blaich, Yvonne Hollenstein, Olivier Dubuis, Michael Nägele, Andreas Buser, Christian H. Nickel, Nicole Ritz, Andreas Zeller, Tanja Stadler, Manuel Battegay, Rita Schneider-Sliwa
bioRxiv 2020.04.03.023135; doi: https://doi.org/10.1101/2020.04.03.023135
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High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters
Adrian Egli, Nina Goldman, Nicola F. Müller, Myrta Brunner, Daniel Wüthrich, Sarah Tschudin-Sutter, Emma Hodcroft, Richard Neher, Claudia Saalfrank, James Hadfield, Trevor Bedford, Mohammedyaseen Syedbasha, Thomas Vogel, Noémie Augustin, Jan Bauer, Nadine Sailer, Nadezhda Amar-Sliwa, Daniela Lang, Helena M.B. Seth-Smith, Annette Blaich, Yvonne Hollenstein, Olivier Dubuis, Michael Nägele, Andreas Buser, Christian H. Nickel, Nicole Ritz, Andreas Zeller, Tanja Stadler, Manuel Battegay, Rita Schneider-Sliwa
bioRxiv 2020.04.03.023135; doi: https://doi.org/10.1101/2020.04.03.023135

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