A new bioinformatic workflow enables streamlined surveillance of pathogen outbreaks

A major challenge during the COVID-19 pandemic was to perform rapid diagnostics of the drastically increased amounts of patient samples. To streamline work procedures, the Department of Clinical Microbiology at Uppsala University Hospital and Clinical Genomics Uppsala developed an automated workflow for data analysis. The workflow includes all analysis steps from pre-processing of sequencing data to annotation of mutations of interest and determination of the lineage of the virus. It is operated through a graphical user interface and can easily be used also by personnel without skills in bioinformatics and programming.

The new workflow enabled faster diagnosis with less hands-on time during the pandemic. This was one of the factors that enabled Uppsala, as one of few regions in Sweden, to perform analysis of all SARS-CoV-2 samples in-house, says René Kaden, leader of the microbiology work package at CG Uppsala and PI of the publication.

In addition to diagnosis of patient samples, the workflow has been used for research projects. It can also be customized for other organisms and can thus be used as a tool for global preparedness in case of future outbreaks of other pathogens.