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Pandemic Preparedness Resources

Metagenomic sequencing for pathogen identification and analysis

PI(s)/Head responsible for the resource:

Jenny Welander

Host organisation(s):

Clinical Microbiology at Linköping University Hospital

Resource description:

Clinical Microbiology at Linköping University Hospital plans to develop a capability to quickly identify and characterize unknown pathogens through metagenomic sequencing. This will enable detection and sequence analysis of pathogens directly from clinical samples of unknown etiology, without the need of pathogen-specific reagents.

Since the middle of June, an M.Sc. in engineering biology has been recruited for the project and is currently learning the already developed methods for whole-genome sequencing of bacteria and target enrichment sequencing of SARS-CoV-2, with supervision from a biologist and a bioinformatician involved in the project.

In parallel, we have started testing three different RNA extraction techniques to optimize RNA isolation from nasopharynx samples.

A literature review has been performed regarding library preparation, and as a result, we have ordered library preparation kits for metagenomic RNA-seq on Illumina and Nanopore. These will be tested and evaluated on human samples with varying concentrations of known viruses (influenza, RS and SARS-CoV-2).

Different bioinformatic approaches will be developed, evaluated and optimized. Once the laboratory and bioinformatic methods are validated on samples of known content, they will be further tested on samples from patients with unknown infections. With this technology development, the laboratory will have an increased preparedness to quickly analyze novel pathogens and to follow and quickly respond to future pandemic situations.

Contact information:

Jenny Welander
Clinical Microbiology at Linköping University Hospital