WILDLIFE RELATED PATHOGEN SURVEILLANCE WITH NANOPORE SEQUENCING OF EDNA SAMPLES: COMPARING IN VITRO AND IN SILICA TARGET ENRICHMENT APPROACHES

INTRODUCTION: Surveillance of wildlife populations for diseases is crucial for the early detection of emerging epidemiological situations, protecting animal conservation efforts and safeguarding the public and animal health. Environmental DNA/RNA (eDNA/eRNA) techniques have gained popularity due to their non-invasive nature and efficiency, making them a valuable instrument for monitoring wildlife-re- lated pathogens (wRP). eDNA offers distinct advantages over conventional direct sampling methods, particularly in the detection of parasitic diseases, where the environment serves as a common reservoir for various parasitic life stages and hosts. with the emergence of portable sequencing technologies, eDNA sequencing has become a leading method for early detection of parasitic infections in wildlife. MATERIALS AND METHODS: This study focuses on eDNA collected from lotic waters in and around La Mandria Regional Park’s fenced-off area (Piedmont region), recognized as one of the primary Eu- ropean hotspots of Fascioloides magna, an invasive trematode of wild and domestic ruminants (bassi, 1875). we employed active targeted surveillance using Nanopore MinION sequencing and evaluated two enrichment strategies: long-range metabarcoding of protist ribosomal subunits (PCR-dependent in vitro target enrichment) and Nanopore’s Adaptive Sampling (PCR-free real-time in silica target enri- chment). RESULTS AND CONCLUSIONS: Our results demonstrate the potential of Nanopore’s Adaptive Sam- pling for efficient, fast, and cost-effective targeted surveillance of parasitic diseases, as evidenced by the difference in detection rates between the two approaches. This suggests a path towards streamlined, real-time in situ genomic-informed surveillance programs