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.

About the Swiss Pathogen Surveillance Platform SPSP

SPSP is a collaborative OneHealth surveillance platform enabling hospital epidemiologists, public health experts and microbiologists/virologists to conduct research, rapidly identify potential outbreaks and take early measures to contain transmission by tracking them in near real-time. SPSP is co-led by SIB together with the University Hospitals of Basel, Lausanne and Geneva, as well as the Universities of Bern and Zurich (see full list of registered groups). It is hosted on SIB’s secure IT infrastructure and complies with the Swiss Personalized Health Network (SPHN) data security standards.

Why virus data need to be made available more openly

Sharing genome sequences from the virus in a way that facilitates their reuse and incorporation in larger datasets is the key to enabling a more representative coverage of emerging variants and anticipation of vaccine efficiency, as well as fundamental research on the evolution of the virus, transmission, etc. A range of platforms allow genomic sequence data to be uploaded, but how the data (and associated metadata) can then be reused by researchers varies. The  European Nucleotide Archive (ENA) has positioned itself as the reference for open sharing of sequence data. As such, ENA provides, together with the assembled sequences, access to the raw data – making it even easier to reuse them. Several calls for COVID-19 data sharing have been issued by the scientific community, such as in an open letter launched by the European COVID-19 Data Portal and supported by SIB (sign the letter), or in a recent opinion piece in Nature.

From viruses to antibiotic-resistant bacteria: a high-resolution surveillance tool for pathogens

Before COVID-19 shuffled research priorities, SPSP’s original purpose was to track the emergence and spread of any pathogens, with an initial focus on multidrug-resistant bacteria. Bringing together research, clinical and veterinary labs, in the future SPSP will allow registered health institutions, for instance, to better understand and track outbreaks other than COVID-19 with high-resolution geographic data, down to the level of postal codes.

With the consortium agreement and ethical approval now validated, registered laboratories across the country can start sending SARS-CoV-2 sequence data, and soon other bacteriological or virological genomic sequences, as well as associated clinical and epidemiological metadata, to SPSP following an approved legal process.

“This is a major breakthrough for Switzerland, which allows us to conduct pathogen research and surveillance at an unprecedented scale across the whole country,” comments Adrian Egli, Head of Bacteriology and Mycology at the University Hospital of Basel and PI of SPSP.

1 Are you a Swiss group/laboratory interested in providing SARS-CoV-2 genomic data to SPSP ? More information