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The Swiss Pathogen Surveillance Platform (SPSP) is a secure One-health online platform that enables near real-time sharing under controlled access of pathogen whole genome sequences (WGS) and their associated clinical/epidemiological metadata.
Metadata are structured using existing ontologies (SNOMED CT, NCBI Taxonomy) and controlled vocabularies whenever possible. WGS are then analyzed using harmonized bioinformatics methods for quality control, assembly, typing and outbreak analyses. Resulting trees are visualized through a local instance of Nextstrain.
The SPSP online portal is hosted at SIB Swiss Institute of Bioinformatics and complies with the Swiss Personalized Health Network (SPHN) data security standards and in particular with the SPHN Information Security Policy (ISP), notably including encrypted transfer and storage of data, and dual-factor authentication.