Viral metagenomics and phylogenomics for One Health

In recent years, the world has faced major health challenges, from the rise of antibiotic resistance to the emergence of new pathogens with pandemic potential. This highlights the importance of considering human health as inextricably intertwined with that of other animals and the environment in which they live. This paradigm is known as “One Health”, which is the integration of environmental sciences, veterinary science, and medicine. Within this perspective, viruses, the most abundant biological entities on Earth, play a central role in connecting different organisms, deeply influencing the health of their hosts. Despite their great importance, most viruses are still poorly understood, mainly because of the technical and economic limitations posed by isolation, cultivation, and single colony sequencing. However, recently developed genomic technologies offer a cheaper and more sensitive alternative to study viruses, allowing a better integration of data from various sources and making it possible to explore how they circulate among different hosts and environments. In this thesis, I hypotesise that, by combining different classes of genomic methods with One Health practices, it is possible to reveal much more of the entire picture of viral diversity and evolution that by simply using them in a separated way. I show that this is the case for each one of the scientific questions addressed in this work, which are organised in three main chapters: - In the second chapter I analysed 22 metatranscriptomes from tick samples from different parts of Italy, obtaining a set of 91 viral contigs for which I reconstructed the phylogeny, with the aim to identify the presence of possible pathogens and characterise the unexplored viral diversity in the country. This analysis not only clarified the molecular epidemiology of well-known pathogens such as Tick-borne encephalitis virus, but also allowed the discovery of at least 10 novel viral species. - In the third chapter, I investigated the origin and spread of West Nile virus, an emerging pathogen causing neurological disease worldwide. The goal was to expand the current knowledge of this virus by increasing the number of sequenced genomes and to reconstruct how the virus moved between Africa and Europe. Phylogeographic and phylodynamic methods showed that this pathogen originated in Africa and repeatedly invaded the European continent, revealing the dynamics of its evolution through space and time. - In the last chapter, I contributed to obtaining a set of DNA phages assembled from human microbiomes and viromes by manual curation and comparative genomics and developed a new approach to study their evolution in relation to their bacterial hosts. I found that the strength of co-phylogenetic patterns between viruses and their hosts is generally weak, suggesting that their ecological relationships emerge on short evolutionary timescales. Taken together, these results show how the integration of viral metagenomics and phylogenomics in One Health is essential to answer fundamental questions about the diversity of viruses and how they spread and evolve. Furthermore, the methods and protocols developed in these studies can be applied to similar cases, allowing a systematic exploration of many other datasets to expand our knowledge of the virosphere. This information can be used to implement containment strategies, public health policies, therapies, and biotechnologies.