Evidence map›Paper›PMID 31434783›Full record

ArticleBMJ open2019

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

Adrian Egli, Claudia Saalfrank, Nina Goldman, Myrta Brunner, Yvonne Hollenstein, Thomas Vogel, Noémie Augustin, Daniel Wüthrich, Helena M B Seth-Smith, Elisa Roth and 16 more

Registry-linked trialAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMJ open, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT03010007 (Prospective Analysis of Seasonal Influenza - Viral Transmission and Evolution in the City of Basel, Switzerland [Prospektive Systemanalyse Der Saisonalen Influenza - Virustransmission Und Evolution in Der Stadt Basel] in German), which is not on this map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

NCT03010007 completednot on this map

Prospective Analysis of Seasonal Influenza - Viral Transmission and Evolution in the City of Basel, Switzerland [Prospektive Systemanalyse Der Saisonalen Influenza - Virustransmission Und Evolution in Der Stadt Basel] in German

TypeobservationalSponsorUniversity Hospital, Basel, SwitzerlandRan2017 to 2018Enrolled800ConditionsInfluenza
3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

26 authors.

Adrian EgliClinical Microbiology, University Hospital Basel, Basel, Switzerland Adrian.Egli@usb.ch.
Claudia SaalfrankHuman Geography, Department of Environmental Science, University of Basel, Basel, Switzerland.
Nina GoldmanHuman Geography, Department of Environmental Science, University of Basel, Basel, Switzerland.
Myrta BrunnerHuman Geography, Department of Environmental Science, University of Basel, Basel, Switzerland.
Yvonne HollensteinBiomedicine, University of Basel, Basel, Switzerland.
Thomas VogelHuman Geography, Department of Environmental Science, University of Basel, Basel, Switzerland.
Noémie AugustinHuman Geography, Department of Environmental Science, University of Basel, Basel, Switzerland.
Daniel WüthrichClinical Microbiology, University Hospital Basel, Basel, Switzerland.
Helena M B Seth-SmithClinical Microbiology, University Hospital Basel, Basel, Switzerland.
Elisa RothClinical Microbiology, University Hospital Basel, Basel, Switzerland.
Mohammedyaseen Syedbasha
Nicola F MuellerSwiss Institute for Bioinformatics, Basel, Switzerland.
Dominik VogtBiomedicine, University of Basel, Basel, Switzerland.
Jan BauerHuman Geography, Department of Environmental Science, University of Basel, Basel, Switzerland.
Nadezhda Amar-SliwaHuman Geography, Department of Environmental Science, University of Basel, Basel, Switzerland.
Dominik M MeinelClinical Microbiology, University Hospital Basel, Basel, Switzerland.
Olivier DubuisMicrobiology, Viollier AG, Allschwil, Basel-Landschaft, Switzerland.
Michael NaegeleMicrobiology, Viollier AG, Allschwil, Basel-Landschaft, Switzerland.
Sarah Tschudin-SutterClinical Research, University of Basel, Basel, Switzerland.
Andreas BuserBlood Donation Center of Both Basel, Basel, Switzerland.
Christian H NickelEmergency Medicine, University Hospital Basel, Basel, Switzerland.
Andreas ZellerCentre for Primary Health Care, University of Basel, Basel, Switzerland.
Nicole RitzPediatric Infectious Diseases and Vaccinology, UKBB Universitats-Kinderspital, Basel, Switzerland.
Manuel BattegayClinical Research, University of Basel, Basel, Switzerland.
Tanja Stadler *Swiss Institute for Bioinformatics, Basel, Switzerland.
Rita Schneider-Sliwa *Human Geography, Department of Environmental Science, University of Basel, Basel, Switzerland.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

introductionUrban 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.

Indexed as

Genome, ViralPopulation SurveillanceClinical Trial Protocols as TopicFemaleHumansInfluenza, HumanMaleObservational Studies as TopicOrthomyxoviridaeRetrospective StudiesSeasonsSwitzerlandWhole Genome Sequencinggeographyinfluenzaquestionnairestudy designtransmissionwhole genome sequencing

Identifiers

PMID31434783
PMCPMC6707652

What OpenQuestion holds

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LicenceCC BY-NC
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Registered trials

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.