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

Clinical Trial Protocols as Topic Female Genome, Viral Humans Influenza, Human / diagnosis Male Observational Studies as Topic Orthomyxoviridae / isolation & purification Population Surveillance Retrospective Studies Seasons Switzerland Whole Genome Sequencing / methods
geography influenza questionnaire study design transmission whole genome sequencing

Journal

BMJ open
ISSN: 2044-6055
Titre abrégé: BMJ Open
Pays: England
ID NLM: 101552874

Informations de publication

Date de publication:
20 08 2019
Historique:
entrez: 23 8 2019
pubmed: 23 8 2019
medline: 1 9 2020
Statut: epublish

Résumé

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. 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. 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. NCT03010007.

Identifiants

DOI: 10.1136/bmjopen-2019-030913 PMID: 31434783 PMC: PMC6707652
pubmed: 31434783
pii: bmjopen-2019-030913
doi: 10.1136/bmjopen-2019-030913
pmc: PMC6707652
doi:

Banques de données

ClinicalTrials.gov
['NCT03010007']

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

e030913

Informations de copyright

© Author(s) (or their employer(s)) 2019. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.

Déclaration de conflit d'intérêts

Competing interests: None declared.

Références

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Auteurs

Adrian Egli (A)

Clinical Microbiology, University Hospital Basel, Basel, Switzerland Adrian.Egli@usb.ch.
Biomedicine, University of Basel, Basel, Switzerland.
Clinical Research, University of Basel, Basel, Switzerland.

Claudia Saalfrank (C)

Human Geography, Department of Environmental Science, University of Basel, Basel, Switzerland.

Nina Goldman (N)

Human Geography, Department of Environmental Science, University of Basel, Basel, Switzerland.

Myrta Brunner (M)

Human Geography, Department of Environmental Science, University of Basel, Basel, Switzerland.

Yvonne Hollenstein (Y)

Biomedicine, University of Basel, Basel, Switzerland.

Thomas Vogel (T)

Human Geography, Department of Environmental Science, University of Basel, Basel, Switzerland.

Noémie Augustin (N)

Human Geography, Department of Environmental Science, University of Basel, Basel, Switzerland.

Daniel Wüthrich (D)

Clinical Microbiology, University Hospital Basel, Basel, Switzerland.
Biomedicine, University of Basel, Basel, Switzerland.
Swiss Institute for Bioinformatics, Basel, Switzerland.

Helena M B Seth-Smith (HMB)

Clinical Microbiology, University Hospital Basel, Basel, Switzerland.
Swiss Institute for Bioinformatics, Basel, Switzerland.

Elisa Roth (E)

Clinical Microbiology, University Hospital Basel, Basel, Switzerland.
Biomedicine, University of Basel, Basel, Switzerland.

Mohammedyaseen Syedbasha (M)

Nicola F Mueller (NF)

Swiss Institute for Bioinformatics, Basel, Switzerland.
Biosystems Science and Engineering, ETH Zurich D-BSSE, Basel, Basel-Stadt, Switzerland.

Dominik Vogt (D)

Biomedicine, University of Basel, Basel, Switzerland.

Jan Bauer (J)

Human Geography, Department of Environmental Science, University of Basel, Basel, Switzerland.

Nadezhda Amar-Sliwa (N)

Human Geography, Department of Environmental Science, University of Basel, Basel, Switzerland.

Dominik M Meinel (DM)

Clinical Microbiology, University Hospital Basel, Basel, Switzerland.
Biomedicine, University of Basel, Basel, Switzerland.

Olivier Dubuis (O)

Microbiology, Viollier AG, Allschwil, Basel-Landschaft, Switzerland.

Michael Naegele (M)

Microbiology, Viollier AG, Allschwil, Basel-Landschaft, Switzerland.

Sarah Tschudin-Sutter (S)

Clinical Research, University of Basel, Basel, Switzerland.
Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland.

Andreas Buser (A)

Blood Donation Center of Both Basel, Basel, Switzerland.

Christian H Nickel (CH)

Emergency Medicine, University Hospital Basel, Basel, Switzerland.

Andreas Zeller (A)

Centre for Primary Health Care, University of Basel, Basel, Switzerland.

Nicole Ritz (N)

Pediatric Infectious Diseases and Vaccinology, UKBB Universitats-Kinderspital, Basel, Switzerland.

Manuel Battegay (M)

Clinical Research, University of Basel, Basel, Switzerland.
Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland.

Tanja Stadler (T)

Swiss Institute for Bioinformatics, Basel, Switzerland.
Biosystems Science and Engineering, ETH Zurich D-BSSE, Basel, Basel-Stadt, Switzerland.

Rita Schneider-Sliwa (R)

Human Geography, Department of Environmental Science, University of Basel, Basel, Switzerland.

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Classifications MeSH

questionsmedicales.fr › Qualité, accès, évaluation des soins de santé › Qualité des soins de santé › Mécanismes d'évaluation des soins de santé › Protocoles cliniques › Protocoles d'essais cliniques comme sujet › Identification of influenza urban transmission...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome viral › Identification of influenza urban transmission...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Identification of influenza urban transmission...
questionsmedicales.fr › Maladies de l'appareil respiratoire › Infections de l'appareil respiratoire › Grippe humaine › Identification of influenza urban transmission...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Caractéristiques des études épidémiologiques › Études cliniques comme sujet › Études observationnelles comme sujet › Identification of influenza urban transmission...
questionsmedicales.fr › Virus › Virus à ARN › Virus à ARN de polarité négative › Orthomyxoviridae › Identification of influenza urban transmission...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Pratiques en santé publique › Surveillance de la population › Identification of influenza urban transmission...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Caractéristiques des études épidémiologiques › Études épidémiologiques › Études de cohortes › Études rétrospectives › Identification of influenza urban transmission...
questionsmedicales.fr › Environnement et santé publique › Environnement › Concepts météorologiques › Atmosphère › Climat › Saisons › Identification of influenza urban transmission...
questionsmedicales.fr › Régions géographiques › Europe › Suisse › Identification of influenza urban transmission...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › Séquençage du génome entier › Identification of influenza urban transmission...