Identification of influenza urban transmission patterns by geographical, epidemiological and whole genome sequencing data: protocol for an observational study
Andreas Buser,
Sarah Tschudin-Sutter,
Adrian Egli,
Claudia Saalfrank,
Nina Goldman,
Myrta Brunner,
Yvonne Hollenstein,
Thomas Vogel,
Noémie Augustin,
Daniel Wüthrich,
Helena M.B. Seth-Smith,
Elisa Roth,
Mohammedyaseen Syedbasha,
Nicola F. Mueller,
Dominik Vogt,
Jan Bauer,
Nadezhda Amar-Sliwa,
Dominik M. Meinel,
Olivier Dubuis,
Michael Naegele,
Christian H. Nickel,
Andreas Zeller,
Nicole Ritz,
Manuel Battegay,
Tanja Stadler,
Rita Schneider-Sliwa
Affiliations
Andreas Buser
10 Department of Hematology, University Hospital Basel, University of Basel, Basel, Switzerland
Sarah Tschudin-Sutter
3 Clinical Research, University of Basel, Basel, Switzerland
Adrian Egli
Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
Claudia Saalfrank
4 Human Geography, Department of Environmental Science, University of Basel, Basel, Switzerland
Nina Goldman
4 Human Geography, Department of Environmental Science, University of Basel, Basel, Switzerland
Myrta Brunner
4 Human Geography, Department of Environmental Science, University of Basel, Basel, Switzerland
Yvonne Hollenstein
2 Biomedicine, University of Basel, Basel, Switzerland
Thomas Vogel
4 Human Geography, Department of Environmental Science, University of Basel, Basel, Switzerland
Noémie Augustin
4 Human Geography, Department of Environmental Science, University of Basel, Basel, Switzerland
Daniel Wüthrich
1 Clinical Microbiology, University Hospital Basel, Basel, Switzerland
Helena M.B. Seth-Smith
1 Clinical Microbiology, University Hospital Basel, Basel, Switzerland
Elisa Roth
1 Clinical Microbiology, University Hospital Basel, Basel, Switzerland
Mohammedyaseen Syedbasha
Nicola F. Mueller
5 Swiss Institute for Bioinformatics, Basel, Switzerland
Dominik Vogt
2 Biomedicine, University of Basel, Basel, Switzerland
Jan Bauer
Division of Health Services Research, Institute of Occupational Medicine, Social Medicine and Environmental Medicine, Goethe-Universitat Frankfurt am Main, Frankfurt, Germany
Nadezhda Amar-Sliwa
4 Human Geography, Department of Environmental Science, University of Basel, Basel, Switzerland
Dominik M. Meinel
1 Clinical Microbiology, University Hospital Basel, Basel, Switzerland
Introduction Urban transmission patterns of influenza viruses are complex and poorly understood, and multiple factors may play a critical role in modifying transmission. Whole genome sequencing (WGS) allows the description of patient-to-patient transmissions at highest resolution. The aim of this study is to explore urban transmission patterns of influenza viruses in high detail by combining geographical, epidemiological and immunological data with WGS data.Methods and analysis The study is performed at the University Hospital Basel, University Children’s Hospital Basel and a network of paediatricians and family doctors in the Canton of Basel-City, Switzerland. The retrospective study part includes an analysis of PCR-confirmed influenza cases from 2013 to 2018. The prospective study parts include (1) a household survey regarding influenza-like illness (ILI) and vaccination against influenza during the 2015/2016 season; (2) an analysis of influenza viruses collected during the 2016/2017 season using WGS—viral genomic sequences are compared with determine genetic relatedness and transmissions; and (3) measurement of influenza-specific antibody titres against all vaccinated and circulated strains during the 2016/2017 season from healthy individuals, allowing to monitor herd immunity across urban quarters. Survey data and PCR-confirmed cases are linked to data from the Statistics Office of the Canton Basel-City and visualised using geo-information system mapping. WGS data will be analysed in the context of patient epidemiological data using phylodynamic analyses, and the obtained herd immunity for each quarter. Profound knowledge on the key geographical, epidemiological and immunological factors influencing urban influenza transmission will help to develop effective counter measurements.Ethics and dissemination The study is registered and approved by the regional ethics committee as an observational study (EKNZ project ID 2015–363 and 2016–01735). It is planned to present the results at conferences and publish the data in scientific journals.Trial registration number NCT03010007.
