Viruses are the most abundant biological entities on Earth and play a fundamental role in shaping microbial ecosystems. They influence the health of oceans, soils, animals and humans by controlling microbial populations and altering how microbes function. Despite their importance, one of the major challenges in microbiology and virology is identifying which viruses infect which host organisms. This “virus–host matching” problem limits our ability to understand microbial ecosystems and prevents the development of predictive tools for microbiome research, biotechnology, and environmental monitoring.
Current approaches mainly rely on indirect computational predictions or ecological correlations, which often lack experimental validation. As a result, a large fraction of viruses discovered through modern sequencing technologies remain unlinked to their biological hosts. This gap represents a major barrier to translating viral diversity data into actionable knowledge.
The VirHoX project addresses this challenge by developing a new experimental and computational framework to directly identify interactions between viruses and their hosts. The project introduces VirHo-seq, an innovative sequencing approach designed to capture molecular evidence of viral–host interactions within cells. By combining new molecular tools, advanced sequencing technologies and dedicated bioinformatic pipelines, VirHoX aims to detect and analyse chimeric RNA molecules that reveal direct links between viral genetic material and host ribosomes.
The project brings together complementary expertise in molecular biology, virology, bioinformatics and systems biology to build a complete workflow for viral–host interaction mapping. The work includes the development of new experimental protocols, the creation of dedicated data analysis tools, and the validation of the technology in model microbial systems.
By enabling the direct identification of virus–host relationships, VirHoX will provide a powerful new capability for microbiome science. The results will help researchers move beyond descriptive studies of viral diversity toward a deeper mechanistic understanding of viral infection processes. In the long term, the knowledge generated by the project can support advances in environmental monitoring, microbiome engineering, and biotechnology applications that rely on controlling microbial ecosystems.
VirHoX also contributes to the broader goals of open science and data sharing promoted by the European Union. The project will produce publicly accessible datasets, protocols and analysis tools that can be used by researchers worldwide. By strengthening Europe’s leadership in advanced molecular technologies and viral ecology, VirHoX aims to create new opportunities for scientific discovery and innovation in the rapidly growing field of microbiome research.
