Advancing genomic epidemiology by addressing the bioinformatics bottleneck: Challenges, design principles, and a Swiss example
Chaoran Chen,
Sarah Nadeau,
Ivan Topolsky,
Niko Beerenwinkel,
Tanja Stadler
Affiliations
Chaoran Chen
Department of Biosystems Science and Engineering, ETH Zürich, Basel, CH 4058, Switzerland; Swiss Institute of Bioinformatics, Lausanne, CH 1015, Switzerland
Sarah Nadeau
Department of Biosystems Science and Engineering, ETH Zürich, Basel, CH 4058, Switzerland; Swiss Institute of Bioinformatics, Lausanne, CH 1015, Switzerland
Ivan Topolsky
Department of Biosystems Science and Engineering, ETH Zürich, Basel, CH 4058, Switzerland; Swiss Institute of Bioinformatics, Lausanne, CH 1015, Switzerland
Niko Beerenwinkel
Department of Biosystems Science and Engineering, ETH Zürich, Basel, CH 4058, Switzerland; Swiss Institute of Bioinformatics, Lausanne, CH 1015, Switzerland
Tanja Stadler
Corresponding author at: Department of Biosystems Science and Engineering, ETH Zürich, Basel, CH 4058, Switzerland.; Department of Biosystems Science and Engineering, ETH Zürich, Basel, CH 4058, Switzerland; Swiss Institute of Bioinformatics, Lausanne, CH 1015, Switzerland
The SARS-CoV-2 pandemic led to a huge increase in global pathogen genome sequencing efforts, and the resulting data are becoming increasingly important to detect variants of concern, monitor outbreaks, and quantify transmission dynamics. However, this rapid up-scaling in data generation brought with it many IT infrastructure challenges. In this paper, we report about developing an improved system for genomic epidemiology. We (i) highlight key challenges that were exacerbated by the pandemic situation, (ii) provide data infrastructure design principles to address them, and (iii) give an implementation example developed by the Swiss SARS-CoV-2 Sequencing Consortium (S3C) in response to the COVID-19 pandemic. Finally, we discuss remaining challenges to data infrastructure for genomic epidemiology. Improving these infrastructures will help better detect, monitor, and respond to future public health threats.