The Clinical Genomics platform plays an important role in technology development at Clinical Microbiology laboratories

In the recent SciLifeLab call for Technology Development Projects (TDPs) within Pandemic Laboratory Preparedness, Clinical Microbiology laboratories have been granted support for analyses of infectious diseases and immune response during infections and vaccination as well as studies on resistance development. The Clinical Genomics platform contributes with sequencing and genomics expertise in these projects.

During the SARS-CoV-2 pandemic, the Clinical Genomics platform quickly contributed to developing and running whole-genome sequencing (WGS) for regional healthcare that proved to be essential for tracking the dynamics of the virus. Now, Clinical Genomics, together with Genomic Medicine Sweden (GMS), will continue to play an important role in pandemic laboratory preparedness and research by providing expertise and services in TDPs at Clinical Microbiology laboratories funded by SciLifeLab.

“Through the Genomics Pandemic Preparedness Portfolio (G3P), which was funded in a previous SciLifeLab call, we have linked together several key genomics infrastructures in Sweden, including the Clinical Genomics platform and the National Genomics Infrastructure at SciLifeLab, the National Pandemic Center and GMS. These new TDPs provide a strong foundation for further developing the national preparedness for future pandemics in collaboration with the Swedish healthcare”, says Valtteri Wirta, PI for G3P and Head of Clinical Genomics Stockholm.

Whole genome sequencing for viral diagnostics

In virology, WGS is crucial to inform the development of novel treatments and vaccines, and increases the resolution of molecular epidemiology and viral genetic variation. However, adoption of WGS in clinical diagnostic laboratories is currently limited.

“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”, says Patrik Medstrand, professor of clinical virology at Lund University and Clinical Microbiology, Region Skåne.

Sensitive and accurate detection of viral pathogens

In addition to WGS, two targeted metagenomic sequencing-based panels will be developed and implemented: a comprehensive panel detecting >3,000 viral species found in both animals and humans and a panel focused on hantavirus.

“With climate change we can anticipate changes in the size and frequency of outbreaks of viral zoonoses, as well as in the spectrum of viral species and their geographical distribution. Thus, the need for fast detection for outbreak investigation will be even more crucial in the future” explains Lisa Pettersson, MD, PhD, Department of Clinical Microbiology, Umeå University Hospital and Umeå University and Head of the Swedish National Reference Laboratory for Hantavirus Infections.

Pre-analytics for pandemic preparedness and metagenomic sequencing

Metagenomics through shotgun sequencing is rapidly expanding as the method of choice for identifying both well-known and emerging pathogens. The pre-analytic sample processing steps are, however, crucial to obtain representative data from the metagenomic analyses.

“For future pandemics, and for studies focusing on the silent pandemic of antibiotic resistance, an optimized pre-analytic standard operating procedure for metagenomic detection of microorganisms and resistance markers will be highly beneficial”, says Martin Sundqvist, MD, PhD, Senior consultant, Dept. Laboratory Medicine, Clinical Microbiology, Örebro University Hospital.

“We are very happy that we can provide both expertise and services to clinical microbiology laboratories across Sweden to promote their work within pandemic preparedness“, concludes Thoas Fioretos, Director of the SciLifeLab Clinical Genomics Platform.

Granted projects in the call for TDPs within Pandemic Laboratory Preparedness at Clinical Microbiology laboratories to which the Clinical Genomics platform will contribute:

• Gothenburg Initiative for Pandemic Laboratory Preparedness, Magnus Lindh, Gothenburg University, Västra Götalandsregionen

• Establishing sequencing-based virology diagnostics for future clinical use: towards pandemic and outbreak preparedness in the clinical laboratory, Patrik Medstrand, Lund University, Region Skåne

• Next generation clinical virology, Tobias Allander, Karolinska Institute, Region Stockholm

• Pre-analytics for Pandemic Preparedness, Martin Sundqvist, Örebro University, Region Örebro län

• Preparedness for tracking resistant and virulent bacterial and fungal pathogens (TRACK-PATH), Christian Giske, Karolinska Institute, Region Stockholm

• Development of a targeted metagenomic NGS platform for diagnostics and epidemiological surveillance of viral pandemic threats, Lisa Pettersson, Umeå University, Region Västerbotten

• Rapid typing of emerging variants in a clinical setting, Anders Bergqvist, Uppsala University, Region Uppsala

• Metagenomic sequencing for pathogen identification and analysis, Jenny Welander, Linköping University, Region Östergötland