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Pandemic Preparedness Capabilities

Genomic Pandemic Preparedness Portfolio (G3P) – Nationally scalable genomics portfolio for detection and surveillance of viral outbreaks

PI(s)/Head responsible for the resource:

Valtteri Wirta

Host organisation(s):

Karolinska Institutet

Resource description:

The current SARS-CoV-2 pandemic highlights the need of building pandemic preparedness capabilities for genetic monitoring (surveillance) of pathogens causing pandemics, as well as early detection of emerging pathogens and antimicrobial resistance in future pandemics and outbreaks. Therefore, our project focus on sequencing-based pandemic preparedness, by developing laboratory assays, along with associated bioinformatics analysis workflows, data visualisation for knowledge sharing and interpretation, and other tools for efficient national coverage.

Developed assays and tools will be established across the SciLifeLab´s Clinical Genomics nodes, Genomic Medicine Centers, and clinical microbiology laboratories to reach national coverage, minimise the distance to point-of-care, and ensuring rapid turnaround times. Methods can aid in testing critically ill patients with diffuse symptoms in non-pandemic situations, and assays will contribute to the SciLifeLab Precision Medicine capability.

Specific aims are to:

  1. Maximise the effects of ongoing efforts by strengthening the national networks and collaborations relevant for pandemic preparedness.

  2. Continue developing whole-genome sequencing-based pathogen surveillance by driving national harmonisation and developing tools for data aggregation and visualisation.

  3. Establish validated metagenomic assays for detection of known and unknown viruses and methods for detecting antimicrobial resistance development.

  4. Coordinate data handling i.e. collection, annotation, structuring and aggregation.

  5. Provide the developed infrastructure as a services regarding wet-lab data generation, bioinformatic analysis, biobanking, and data standardisation, for the research community, healthcare and public health authorities.

This resource involves three subprojects:

1. Highly parallelised multi-taxonomic profiling of shotgun metagenomic data (taxprofiler)

For more information on Taxprofiler (including information on access, use, and contact), please see the dedicated Taxprofiler.

2. SARS-CoV-2 bioinformatics pipeline – GMS Artic

For more information on GMS Artic (including information on access, use, and contact), please see the dedicated GMS Artic page.

3. SARS-CoV-2 Reporter for visualisation of SARS-CoV-2 genome sequence data (SC2reporter)

For more information on SC2reporter (including information on access, use, and contact), please see the dedicated SC2reporter page.

Contact information:

Valtteri Wirta
Director, Clinical Genomics facility