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Pandemic Preparedness Capabilities

Gothenburg initiative for pandemic laboratory preparedness (GILP)

PI(s)/Head responsible for the resource:

Magnus Lindh

Host organisation(s):

Dept. of Clinical Virology, University of Gothenburg and Clinical Microbiology, Sahlgrenska University Hospital

Resource description:

Clinical Microbiology, Sahlgrenska University Hospital (CMSU) is one of the largest microbiology laboratories in northern Europe. It provides microbiological diagnostics to a population of 1.2 million people and collaborates with the Institute of Biomedicine, University of Gothenburg, on a broad range of research projects, including several on Covid-19. During the Covid-19 pandemic CMSU was the first hospital laboratory in Sweden to offer SARS-CoV-2 RNA testing and the first to provide test results on mobile phones.

We have resources such as deep sequencing instruments and bioinformatics, but further development is important for pandemic laboratory preparedness. For this aim, established routines that provide us with waste water specimen and clinical samples, are important. The technologies and expertise in ongoing research are also critical.

We will use and develop these resources further to establish a pandemic preparedness. Specifically we will:

  1. Develop and expand our metagenomics microbial monitoring on waste water to include broad searches for emerging pathogens. This will be achieved by improved enrichment of viral nucleic acids, greater sequencing depth and refined bioinformatics searches.

  2. Develop and expand metagenomics microbial monitoring on clinical samples by similar strategies.

  3. Refine a bioinformatics tool for genomic signatures.

  4. Develop bioinformatic search algorithms for minor viral subtypes,

  5. Expand a high-throughput T cell assay pipeline for additional viruses.

  6. Further develop our BSL3 competence for viral culture, neutralisation and antiviral assays.

Continuation funding:

This capability received funding from the REPLPCM call to continue their work. Please see our PLP background information page for more information about the REPLPCM call. With the funding, the capability is developing metagenomics methods for clinical samples, as this will become increasing important in diagnostics. The transfer to the Illumina platform will reduce the cost and improve performance by refining bioinformatics. The capability will also continue to develop existing methods used with processing wastewater, viral culture, and genomic signature analyses. Further, studies of ADAR-induced mutations and minor quasispecies will be expanded, by also using long-read platforms (PacBio) and investigating mutations induced by APOBEC. T cell assays will also be further developed and applied.

Contact information:

Magnus Lindh
Dept. of Clinical Virology, University of Gothenburg and Clinical Microbiology, Sahlgrenska University Hospital