Open-SPSP: A Swiss-wide platform to open viral and bacterial sequences and clinical/epidemiological data to researchers world-wide, while preserving patient privacy
With this project, SPSP enabled large-scale data sharing and validation for SARS-CoV-2, processing over 100,000 samples in 2021. Tools for batch uploads, metadata checks, and ENA export were developed. With 90,000+ open sequences published, SPSP became a European model for open genomic data sharing and standardization.
Project description
To respond efficiently to outbreaks and pandemics such as Covid-19, open and rapid access of
researchers to sequencing data produced at clinical centers is essential, as exemplified by the UK
mutation uncovered in December. Currently, national SARS-CoV-2 data hubs organise the flow of viral
sequences coming from laboratories all over Europe to a central European portal via the European
Nucleotide Archive (ENA). These open resources allow reusing and analyzing the data to researchers
world-wide. Unfortunately, Switzerland does not have such a national data hub that facilitates Open
sharing of data, likely explaining that less than 600 sequences were published on the Covid-19 portal
so far. In order to enable Swiss clinical laboratories to submit in a few clicks, in real-time, their
sequences to ENA, we propose to extend the existing “Swiss Pathogen Surveillance Platform”, a
secure online platform for pathogen sequencing data and their associated sensitive
clinical/epidemiological metadata.
This will not only allow incorporating Swiss data in research projects
worldwide, it will also bring Switzerland within the network of national data hubs for future strategic
developments. With this project, we will in particular (i) facilitate the data upload to SPSP to foster near
real-time data submissions with optimized e-accessibility. (ii) Develop a module to automatically
publish to ENA genomic data and their associated, non-sensitive, metadata. Reciprocally, we will also
import into SPSP the genomes available on NCBI/ENA with their limited metadata to enable Swiss
researchers to address research questions using the rich metadata on Swiss strains alongside strains
collected elsewhere. (iii) Setup a secure computation server with analysis tools, for users with ethical
approvals to address research questions on SPSP sensitive data that could not be published on ENA.
Altogether, our project will make SPSP data Open when possible, and FAIR where patient-privacy
issues apply.
Results
As of May 2025, SPSP is still one of the top SARS-CoV-2 open data submitters to the European Covid-19 Data Portal.
