The question is not whether the world will face another pandemic, but when. SIB is at the heart of efforts to improve epidemic preparedness, building on work during COVID-19 – which helped establish Switzerland as a world leader for pathogen surveillance and data-informed responses.
Reinforcing national and global infrastructures for pathogen data
SIB’s Centre for Pathogen Bioinformatics coordinates a sustainable ecosystem of tools and experts for ongoing genomic surveillance of any pathogen of concern. These take a One Health approach that considers interactions between human, animal, and environmental health – and can be quickly mobilized to respond to infectious disease outbreaks and epidemics.
Successes and ongoing projects for epidemic preparedness include:
- coordinating the strategic development of key tools and databases for storing, analysing, sharing, visualizing and interpreting pathogen genomic data;
- centralizing and standardizing all genomic sequences collected in Switzerland for three respiratory viruses and a food-borne pathogen through an expanded Swiss government mandate for one of these databases, the Swiss Pathogen Surveillance Platform (SPSP);
- enabling wastewater monitoring at the national and international level;
- supporting global infectious disease research and public health responses through the Pathogen Data Network (PDN).
Work is also underway for SPSP to support new EU food safety requirements as the Swiss national depository for genomic sequences of microorganisms used in the food chain.
Spotlight: catching outbreaks early through wastewater surveillance
Pathogens can often be detected in wastewater before clinical cases start rising. This provides a cost-effective way to monitor circulating strains at scale – and gives health authorities and hospitals time to mitigate the impact of a new outbreak or variant, such as by preparing vaccines and stocking treatments.
SIB scientists support wastewater surveillance at the national and international level.
- Providing data analyses and reports for Switzerland’s wastewater monitoring system. Genome sequences from routine wastewater samples collected by Eawag are analysed to detect genomic variations and track variant evolution in real time, by the SIB NEXUS Personalized Health and Computational Biology groups using SIB Resources (V-pipe, Nextclade and Nextstrain). The reports are shared with the Federal Office of Public Health, feeding its Infectious Disease Dashboard, and made openly available on the Swiss Pathogen Surveillance Platform, another SIB Resource. Four viruses – SARS-CoV-2, RSV, influenza A and influenza B – are currently monitored.
- Advancing wastewater surveillance through the Pathogen Data Network. The work includes enabling wastewater-based analysis of bacterial, fungal, and parasitic pathogens (IMMense, developed by SIB scientists), creating publicly available, interactive wastewater dashboards (GenSpectrum, supported by Loculus and V-pipe; all developed by SIB scientists), and providing recommendations to the US National Wastewater Surveillance System.
Harnessing COVID-19 learnings in public outreach
SIB scientists developed a digital workshop for students and the public to help explain the crucial role bioinformatics played during the pandemic, from understanding the virus’ biology and tracing its evolution to monitoring its presence in wastewater.
Building on bioinformatics tools developed for SARS-CoV-2
The Centre for Pathogen Bioinformatics builds on resources and expertise built during the COVID-19 pandemic – which continue to serve as key tools in national and international genomic surveillance systems for SARS-CoV-2.
Harnessing COVID-19 learnings in public outreach
SIB scientists developed a digital workshop for students and the public to help explain the crucial role bioinformatics played during the pandemic, from understanding the virus’ biology and tracing its evolution to monitoring its presence in wastewater.
Our pandemic contributions include:
- providing the Swiss national infrastructure for SARS-CoV-2 genomic sequences;
- developing many other databases and tools to monitor the virus’ evolution and spread and understand its biology;
- facilitating international open sharing of SARS-CoV-2 genomic sequences as co-lead of the ELIXIR CONVERGE project;
- enabling faster drug discovery as part of the European public-private Exscalate4CoV consortium.
As far as I know, every country with a national SARS-CoV-2 surveillance system has relied on SIB tools.
In-depth features on epidemic preparedness
- Around COVID-19 – SIB Profile 2021
- Preparing for the next epidemic – SIB Profile 2025
