With a large part of our knowledge of the world’s species buried in the literature, accessing accurate information (e.g. species name, genetics and ecological information) is not a trivial task. Reliable and accessible references are thus crucial, whether for monitoring species through their DNA footprint or for tracking pathogen evolution. They also underpin community efforts to fulfil the biodiversity restoration objectives from COP15, for instance. Find out how resources and methods developed at SIB tackle such roadblocks to advance knowledge on human, animal and environmental health.
Some of the major roadblocks hindering One Health projects
- Data heterogeneity: data vary in type, scope and scale, requiring harmonization
- Data paucity: data suffer from many gaps, requiring imputation or modelling
- Data quality/resolution: production technologies vary, requiring curation and standards
- Data integration: incompatibility between data requires their FAIRification
Detailed information about viruses according to their host organism
The expertly curated resource ViralZone, developed at SIB’s Swiss-Prot group, includes factsheets for viruses infecting animals, plants, microorganisms, etc. This includes 64 viruses that infect humans from animals (i.e. zoonoses). These viruses are the most likely to spill over and develop human-to-human transmission before becoming endemic. This is what happened with SARS-CoV-2, most likely from bats.
Some of the major roadblocks hindering One Health projects
- Data heterogeneity: data vary in type, scope and scale, requiring harmonization
- Data paucity: data suffer from many gaps, requiring imputation or modelling
- Data quality/resolution: production technologies vary, requiring curation and standards
- Data integration: incompatibility between data requires their FAIRification
Examples of viruses from animals infecting humans. From left to right: H5N1, tick-borne encephalitis, monkey pox
However crucial for One Health, the development and adoption of standards, protocols or guidelines should not be on the shoulders of individual researchers, but of a dedicated research infrastructure. This is part of the ambition of the Biodiversity Genomics Europe project, in which SIB participates. It is also what SIB’s Environmental Bioinformatics group is meant to contribute to.
Monitoring species DNA in the environment: not without the right infrastructure
Environmental DNA – or eDNA – allows researchers to detect and monitor the presence of various organisms, including pathogens, plants, animals and microbes, without the need for direct observation, for instance from water or droppings. But with sometimes very low amounts of DNA, the nature of the data requires a solid bioinformatics infrastructure (e.g. analysis pipelines and modelling approaches), such as that developed at SIB, to produce reliable results. It also relies on good-quality reference data, which is part of what the European Reference Genome (ERGA) project, chaired by SIB’s Robert Waterhouse, is set to establish.
A new resource to query scientific papers on One Health issues: filling a key gap
To address the current gap in literature libraries on ecology and environmental papers, a dedicated resource, BiodiversityPMC, was developed by the SIB Group led by Patrick Ruch, together with Plazi and the publisher Pensoft. This resource mines the literature to enable users to answer a wide range of biodiversity questions related to human health such as:
- Which evidence supports the idea that pangolins and bats interact?
- Which species are reservoir hosts to the tick?
We are looking forward to developing computational technologies allowing the expansion of the genomic monitoring and real-time analysis currently conducted on SARS-CoV-2 to other important pathogens such as influenza and RSV, by leveraging the SIB network of expertise and multidisciplinary partnerships.
Monitoring pathogens in Swiss wastewater: a collaborative effort
The passive monitoring of SARS-CoV-2 in wastewater is a cornerstone of the current surveillance strategy of the FOPH, in the absence of broad clinical testing. This monitoring enables early warning of the introduction of new variants, provides estimates of their spread and evaluates epidemiological characteristics, earlier than traditional clinical surveillance and at a fraction of the cost. This stream of data converges with the SPSP for their open publication on the European Nucleotide Archive according to international standards.
SIB groups involved:
- Computational Biology group (ETH Zurich), developing the SIB Resource V-pipe
- Computational Evolution group (ETH Zurich)
- Functional Genomics Center Zurich (ETH Zurich / University of Zurich)
- NEXUS Personalized Health Technologies (ETH Zurich)
Other institutions involved:
EAWAG, ETH Zurich / University of Basel, EPFL, Biosafety Laboratory (Basel-Stadt) and Microsynth AG.
A suite of leading complementary data analysis tools to track COVID-19 and other pathogens
- Nextstrain (developed by Richard Neher’s group at SIB) was a key surveillance tool during, but also before the pandemic. It is also notably used to track influenza variants and supports yearly vaccine development.
- covSPECTRUM (developed by Tanja Stadler’s group at SIB) enables the extraction of temporal analytics on the circulating variants and mutations.
- CoVariants (developed by Emma Hodcroft's group at SIB) is a trusted reference for the overview of SARS-CoV-2 variants and mutations and was the first variant-tracking website.
- V-pipe (developed by Niko Beerenwinkel’s group at SIB) allows for early detection and quantification of SARS-CoV-2 genomic variants in wastewater and estimation of their relative fitness advantages.
- ViralZone (developed by SIB’s Swiss-Prot group) presents curated information on the virus’s proteins.
Microbes have no borders: international cooperation is key
In Switzerland and internationally, there is growing recognition of the need to bring together researchers and practitioners across institutions to coordinate efforts and address environmental challenges. In addition to supporting international research, SIB is playing an active role in international initiatives related to One Health:
- SIB co-leads ELIXIR’s priority area on “Biodiversity, Food Security and Pathogens” for the Scientific Programme 2024-2028.
- SIB co-led the ELIXIR CONVERGE WP9 initiative aimed at mobilizing European SARS-CoV-2 genomic data from 20+ national genomic surveillance programmes and that plans to federate national data hubs beyond COVID-19.
- Drawing on its European coordination experience, SIB was asked to lead an NIH grant proposal for pathogen surveillance with a global impact involving 11 countries and 12 institutions.
