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.
Study Type
OBSERVATIONAL
Enrollment
4,000
Similarity of Influenza viruses
Genomic sequencing of single virus of individual patients and comparison of genetic similarity of viruses. Grouping of patients with a same virus - this includes a range of single nucleotide polymorphisms of 0-150 differences inbetween the virus population.
Time frame: at baseline
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