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Identification of influenza urban transmission patterns by geographical, epidemiological and whole genome sequencing data: protocol for an observational study

Egli, Adrian and Saalfrank, Claudia and Goldman, Nina and Brunner, Myrta and Hollenstein, Yvonne and Vogel, Thomas and Augustin, Noémie and Wüthrich, Daniel and Seth-Smith, Helena M. B. and Roth, Elisa and Syedbasha, Mohammedyaseen and Mueller, Nicola F. and Vogt, Dominik and Bauer, Jan and Amar-Sliwa, Nadezhda and Meinel, Dominik M. and Dubuis, Olivier and Naegele, Michael and Tschudin-Sutter, Sarah and Buser, Andreas and Nickel, Christian H. and Zeller, Andreas and Ritz, Nicole and Battegay, Manuel and Stadler, Tanja and Schneider-Sliwa, Rita. (2019) Identification of influenza urban transmission patterns by geographical, epidemiological and whole genome sequencing data: protocol for an observational study. BMJ Open, 9 (8). e030913.

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Official URL: https://edoc.unibas.ch/71785/

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Abstract

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.
Faculties and Departments:03 Faculty of Medicine > Bereich Kinder- und Jugendheilkunde (Klinik) > Kinder- und Jugendheilkunde (UKBB) > Infektiologie und Vakzinologie (Heininger/Rudin)
03 Faculty of Medicine > Departement Klinische Forschung > Bereich Kinder- und Jugendheilkunde (Klinik) > Kinder- und Jugendheilkunde (UKBB) > Infektiologie und Vakzinologie (Heininger/Rudin)
03 Faculty of Medicine > Bereich Medizinische Fächer (Klinik) > Infektiologie > Infektiologie (Battegay M)
03 Faculty of Medicine > Departement Klinische Forschung > Bereich Medizinische Fächer (Klinik) > Infektiologie > Infektiologie (Battegay M)
03 Faculty of Medicine > Bereich Medizinische Fächer (Klinik) > Institut für Hausarztmedizin IHAMB
03 Faculty of Medicine > Departement Klinische Forschung > Bereich Medizinische Fächer (Klinik) > Institut für Hausarztmedizin IHAMB
03 Faculty of Medicine > Bereich Querschnittsfächer (Klinik) > Labormedizin > Klinische Mikrobiologie (Frei)
03 Faculty of Medicine > Departement Klinische Forschung > Bereich Querschnittsfächer (Klinik) > Labormedizin > Klinische Mikrobiologie (Frei)
03 Faculty of Medicine > Departement Biomedizin
03 Faculty of Medicine > Departement Biomedizin > Department of Biomedicine, University Hospital Basel > Applied Microbiology Research (Egli)
03 Faculty of Medicine > Departement Klinische Forschung
05 Faculty of Science > Departement Umweltwissenschaften > Geographie > Humangeographie / Stadt- und Regionalforschung (Schneider-Sliwa)
UniBasel Contributors:Vogel, Thomas and Egli, Adrian and Saalfrank, Claudia and Goldman, Nina and Brunner, Myrta and Hollenstein, Yvonne and Augustin, Noémie Anja and Wüthrich, Daniel and Seth-Smith, Helena and Roth, Elisa and Syedbasha, Mohammedyaseen and Vogt, Dominik and Bauer, Jan and Sliwa, Nadezhda and Meinel, Dominik and Buser, Andreas S. and Nickel, Christian and Zeller, Andreas and Ritz, Nicole and Battegay, Manuel E. and Schneider-Sliwa, Rita and Stadler, Tanja
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:BMJ Publishing Group
e-ISSN:2044-6055
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:12 Nov 2019 13:10
Deposited On:12 Nov 2019 13:10

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