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Testing a RNA Depletion Technique to Increase Virus Capture from Nanopore Sequencing of Avian Samples
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Harris, Stephen E.
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Spring 2025
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2025
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10144_Daniel_Tucci.pdf
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Emerging infectious diseases, the majority of which originate from animals, underscore the need for efficient wildlife viral surveillance. Waterfowl, particularly migratory species, serve as reservoirs and potential vectors for a wide range of viruses, including zoonotic and invertebrate-associated pathogens. This study evaluated a targeted RNA depletion technique coupled with Oxford Nanopore MinION sequencing to enhance viral detection in avian samples collected along the Atlantic Flyway. Using oligonucleotide probes targeting ribosomal RNA, followed by enzymatic digestion and bead purification, we enriched for non-rRNA sequences in viral RNA extracts. Subsequent sequencing revealed a diverse virome, with significant representation from bacteriophages, zoonotic mammarenaviruses, and invertebrate-associated viruses such as White Spot Syndrome Virus and Cyprinid herpesvirus 3. More notably, avian-specific viruses were infrequently detected, suggesting many viruses may have been acquired through trophic exposure rather than active infection. Our approach successfully identified low-abundance viral RNA, demonstrating its applicability for field-based wildlife virome studies and its relevance to One Health frameworks. Future work should explore seasonal and geographic variation, host-parasite interactions, and the role of migratory birds as ecological vectors in global pathogen dynamics.
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