Prospective System Analysis of the Seasonal Influenza Virus Transmissions and Evolution in the City of Basel Basel

Prospective System Analysis of Seasonal Influenza - Virus Transmission and Evolution in Basle Town

The project aims to use epidemiological tools to understand the transmission and evolution of influenza viruses at an individual and population level within a small-scale city (Basel) through a combination of experimental, clinical, and mathematical advances. Investigators aim to quantitatively characterize the viral transmission using novel molecular-epidemiological tools based on whole genome sequencing.

Samples will be collected such as whole blood, serum and DNA, nasopharyngeal swamps to diagnose influenza by polymerase chain reaction (PCR) and to determine colonization rates with Staphylococcus aureus and Streptococcus pneumonia. All samples except the first naso-pharyngeal swab for influenza diagnostics will be stored in a biobank and analysed in batches. Each influenza virus isolate will be sequenced using a "whole genome sequencing" approach. The viral transmission and evolution will be analysed using whole genome data for a detailed molecular and phylogenetic tree analysis, respectively. The epidemiological and geographical data will be incorporated into the phylogenetic model.

Inclusion Criteria:

• Each pediatric or adult patient, which fulfill the World Health Organization (WHO) definition of Influenza like illness.
• The case definition includes an acute respiratory infection with coughing, fever ≥38°C, and start of symptoms within the last 10 days.
• Presentation of the patient with influenza-like illness on the emergency ward of the University Hospital Basel or the University Children Hospital of both Basel or a collaborating private practise.

Exclusion Criteria:

- Case definition for influenza like illness is not fulfilled