Over the past weeks and with the threat of emerging variants growing, pressing calls for an open sharing of SARS-CoV-2 sequencing data were issued by the scientific community. Such sharing would allow fast, representative and large-scale research on the virus – but infrastructure and the corresponding investments are often lacking. Echoing these calls, the Swiss Pathogen Surveillance Platform (SPSP) co-led by SIB is now supported by the Swiss Federal authorities to act as the Swiss SARS-CoV-2 Data Hub. Initially developed to track the emergence and spread of any pathogens in Switzerland, SPSP has developed into a user-friendly platform to collect viral genome sequences produced from Swiss samples in the context of the pandemic and submit them notably to the European Nucleotide Archive (ENA), the reference for open sharing of sequence data.
Plugging Swiss open data into global efforts with a Swiss SARS-CoV-2 Data Hub
Recognizing the value that SPSP (see box) represents for Swiss-generated data in this context, the Swiss Federal authorities, through the State Secretariat for Education, Research and Innovation SERI, support its specific use for the sharing of viral sequences with the international community. SPSP thus serves as a Swiss SARS-CoV-2 Data Hub: any research or clinical laboratory sequencing the genome of the virus from positive tests will submit to SPSP1, which will annotate the data and push the viral sequences, together with associated non-sensitive metadata, to ENA and GISAID, the two major repositories of sequence data on the virus to date.
“Through SPSP, Switzerland has just connected its scientific community to the international open data-sharing efforts to boost research on the virus – and the tracking of its evolution,” says Aitana Lebrand, Team Lead Data Science at SIB and co-PI of SPSP. In the near future, the consortium may also report and notify new variants to the Federal Office of Public Health.