Pathogen surveillance

What is pathogen genomic surveillance?

Pathogen genomic surveillance refers to the continuous monitoring and analysis of the genetic material of viruses, bacteria, and other infectious agents. This approach enables the tracking of how pathogens evolve, spread, and adapt over time.

A genomic surveillance strategy enables public health authorities to:

    • detect outbreaks at an early stage;
    • identify emerging variants and drug-resistant strains;
    • understand transmission patterns in communities;
    • inform diagnostics, treatments, and vaccination strategies.

Pathogen genomic surveillance is essential during public health crises and in ‘peace’ time. Indeed, genomic surveillance played a critical role during the COVID-19 pandemic but remains essential today. It supports public health responses to both emerging and endemic diseases, from respiratory infections to antimicrobial resistance. In Switzerland, it includes data from clinical and environmental sources, including wastewater.

An accurate and fast answer to any human or animal infectious disease needs high quality, centralised data. To enable this, an integrated infrastructure such as SPSP is essential, to protect public health and maintain economic stability, by facilitating coordinated interventions of public health authorities, connecting laboratories and research institutions across the country, and providing high-quality, curated data from both clinical and environmental sources.

“Data sharing is caring. SPSP allows important and rapid data exchange in critical public health situations but also to improve our diagnostics.”

Adrian Egli 
Chair of SPSP
Director, Institute of Medical Microbiology, UZH

SPSP: a robust system to support pathogen genomic surveillance

SPSP is the national platform to support pathogen surveillance programmes, real-time monitoring of outbreaks and of circulating strains. Its integrated approach ensures a more comprehensive, real-time picture of infectious disease dynamics.

As the National SARS-CoV-2 Data Hub, SPSP served as a model of data governance and coordination to inspire the development of other national data hubs across Europe (read more). It is also one of the core resources of the Centre for Pathogen Bioinformatics, whose aim is to ensure that Switzerland remains at the forefront of data management and data analysis required for real-time surveillance.

These initiatives, including the International Pathogen Surveillance Network (IPSN) of the World Health Organization, rely on sustained national investment and collaboration.

Learn more about SPSP