Next generation clinical virology

PI(s)/Head responsible for the resource:

Tobias Allander

Host organisation(s):

Karolinska Institutet

Resource description:

Diagnostic metagenomic next-generation sequencing (mNGS) is a rapidly developing cutting-edge method for diagnosis of infectious diseases. It has the potential for unbiased, hypothesis-independent detection of all infectious agents. In addition, it can provide genotyping and susceptibility prediction as well as information about the patient’s immunological response to the infection. It also has the advantage of detecting new infectious agents, and is therefore widely recognised as an important component of pandemic preparedness. With the support of PLP funding, Clinical Microbiology at Karolinska University Hospital and Clinical Genomics Stockholm/GMCK have established a diagnostic mNGS service which is regularly used by health care providers nation-wide and increasingly also by clinical researchers. We will continue to improve this diagnostic workflow (shortened analysis time and improved sensitivity, both by use of Illumina and Nanopore sequencing) and establish systematic secondary research use of generated diagnostic data, including analysis of unclassified sequences, data on ubiquitous viruses, and human transcriptome data. More systematic use of these data can improve the diagnostic value of diagnostic metagenomics, improve the ability to detect new pathogens, and help generating new hypotheses on the association between viruses and disease.

Contact information:

Tobias Allander
Karolinska Institutet
Email: tobias.allander@regionstockholm.se