Workpackage 5

From comparable data to actionable information: Additional tools for detection of and response to (re-) emerging infections

WP leader: Ron Fouchier, EMC (2) r.fouchier@erasmusmc.nl
co-leader: Mark Woolhouse, UEDIN (11) mark.woolhouse@ed.ac.uk

Overall task: To develop cross-sector and cross-pathogen methods for support of emerging pathogen identification and characterization in support of outbreak investigations and epidemiological analysis.

1. To develop an analytical framework for detection of (re-) emerging pathogens in metagenomic datasets.

2. To develop tools for rapid sequence-based detection of strain-specific clusters in time, place and host for the main emerging pathogen classes.

3. To develop tools for fast and robust phylogenetic and phylogeographic analysis.

4. To develop tools for detecting single nucleotide polymorphisms in pathogen NGS data.

5. To improve the prediction of phenotype changes related to antigenicity, drug-resistance, virulence, transmission, and other traits from nucleotide sequence data.