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Pandemic Preparedness Resources

Establishing sequencing-based viral diagnostics for future clinical use: towards pandemic and outbreak preparedness in the clinical laboratory

PI(s)/Head responsible for the resource:

Patrik Medstrand

Host organisation(s):

Clinical Virology, Lund University and Clinical Microbiology, Medicinsk Service, Region Skåne

Resource description:

This proposal builds on the collaboration between the Dept. of Clinical Microbiology at Region Skåne, the Dept. of Translational Medicine, Section of Clinical Virology at Lund University, and Clinical Ge- nomics Lund at SciLifeLab, to develop and disseminate new state-of-the-art viral diagnostics meth- ods for improved Swedish healthcare. This collaboration already successfully established and im- plemented whole-genome sequencing (WGS) of SARS-CoV-2 during the pandemic (since February 2021).

WGS of pathogens is becoming increasingly important for clinical science and practice. Moreover, as witnessed by the current pandemic, WGS has proven to be indispensable for tracking the dynam- ics of SARS-CoV-2 and will be similarly crucial for emerging outbreaks. However, the adoption of WGS in clinical diagnostic laboratories is currently limited and very few WGS protocols for other viruses have been validated for clinical use. In virology, WGS is crucial to inform the development of novel treatments and vaccines, and increases the resolution of molecular epidemiology (for example, in nosocomial transmission) and viral genetic variation as exemplified by the current pandemic. We envision that routine establishment of WGS-based diagnostics of viruses in a clinical setting will become increasingly important for patient care and the wider society, which also will contribute to Pandemic Laboratory preparedness. This proposal specifically aims to accelerate the development of laboratory and bioinformatic WGS protocols in a clinical diagnostic setting for a large number of viruses, to train personnel and increase know-how of WGS in the clinical laboratory, and facilitate data sharing.

Contact information:

Patrik Medstrand
Clinical Virology, Lund University and Clinical Microbiology, Medicinsk Service, Region Skåne