Skip to main content

Pandemic Preparedness Capabilities

Rapid establishment of comprehensive laboratory pandemic preparedness – RAPID-SEQ

Funding given for project project entitled:

Rapid establishment of comprehensive laboratory pandemic preparedness – RAPID-SEQ

PI(s)/Head responsible for the resource:

Jan Albert

Host organisation(s):

Karolinska Institutet

Resource description:

The constant emergence and replacement of new SARS-CoV-2 variants has shown the need for continuous large-scale surveillance to monitor for future pandemic threats. This project builds on established collaboration between SciLifeLab and the Karolinska University Laboratory, and provide samples, data and expertise from Sweden’s largest microbiology laboratory. In addition, the structure is part of Genomic Medicine Sweden (GMS) which is ensuring the coordination with other national efforts.

The laboratory has established large-scale WGS of SARS-CoV-2. To-date 40,000+ samples sequenced and reported to SMInet and GISAID (capacity 500 WGS/week). The RAPI-SEQ project has generated several papers on SARS-CoV-2 variants and neutralisation.

Metagenomics has been established as a clinical diagnostic tool as well as preparedness for rapid identification of new pandemic threats.

This project involves two subprojects; taxprofiler and GMS Artic. Please see the taxprofiler and GMS Artic pages for more information (including information on access and usage).

Specific project aims:

  1. An infrastructure for sample handling and sequencing, with access to BSL-2/3 labs, metadata, automation, etc.
  2. High-capacity, short-read and long-read sequencing for rapid continuous surveillance of emerging SARS-CoV-2 variants linked with capacity for functional tests.
  3. Establishment of a metagenomic assay for molecular surveillance of respiratory viruses
Contact information:

Jan Albert