Achievements and legacy of the largest SARS-CoV-2 sequencing effort in Switzerland

On 17 April, a scientific symposium was held at D-BSSE to acknowledge and celebrate the completion of this massive collaborative effort. In attendance at the symposium were core team members from the research groups led by Tanja Stadler at D-BSSE, the ETH Platforms NEXUS Personalized Health Technologies and the Scientific IT Services, as well as representatives from the diagnostic laboratory Viollier AG, high-throughput sequencing centres including the Genomics Facility Basel and the Functional Genomics Centre Zurich, the Swiss Pathogen Surveillance Platform, the Swiss Institute of Bioinformatics, and the Federal Office of Public Health.

In March 2020, it all started with an impromptu phone call that led to a collaboration between D-BSSE and Viollier AG to sequence SARS-CoV-2 genomes from positive tests. From these humble beginnings the collaboration grew to become the biggest SARS-CoV-2 sequencing effort in Switzerland and left an enormous legacy: 76’922 publicly available SARS-CoV-2 genomes, representing nearly half of all Swiss SARS-CoV-2 genomes sequenced until the end of 2022. Importantly, the consortium was the only Swiss effort to do weekly sequencing throughout 2020, and the resulting genomic data represents an invaluable resource for studying the early spread of the virus in the country.