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Pandemic Preparedness Capabilities

Towards clinical-grade host response diagnostics for pandemic preparedness


PI(s)/Head responsible for the resource:

Niklas Björkström

Host organisation(s):

Karolinska Institutet

Resource description:

This project addresses an unmet clinical and technological need in pandemic preparedness; the absence of clinically scalable, host-directed diagnostics that can guide treatment decisions in severe viral infections. During the COVID-19 pandemic, while viral detection tools were rapidly deployed, diagnostics reflecting the patient’s immune response lagged behind, despite their potential to support triage and inform immunomodulatory therapy. Corticosteroids such as dexamethasone remain a cornerstone in the treatment of subgroups of patients with severe viral pneumonia, but their benefit is highly context-dependent and may be harmful in some patients. The lack of biomarkers to guide their use remains a critical clinical gap.

To meet this need, we will develop and validate a clinically applicable transcriptomic platform for host response diagnostics in viral pneumonia, with a specific focus on corticosteroid responsiveness. The technological approach centers on bulk RNAseq from peripheral blood, adapted for diagnostic workflows in hospital laboratories. In Aim 1, we will work toward developing a streamlined RNAseq pipeline, optimising sample handling, turnaround time, and bioinformatic interpretation in collaboration with clinical labs at Karolinska, Sahlgrenska, and Skåne University Hospitals. In Aim 2, we will validate predefined host response signatures using biobanked samples from influenza patients enrolled in the ongoing RECOVERY trial, linking transcriptomic data to clinical outcomes and treatment benefit.

The platform will be developed with compatibility for future regulatory approval and national scaling in mind, using infrastructure from Clinical Genomics at SciLifeLab. Outputs will support preparedness for future pandemics and have broader relevance for other immune-mediated infectious diseases.

Contact information:

Niklas Björkström
Karolinska Institutet
Email: Niklas.bjorkstrom@ki.se