Discovery of Novel Viruses and Common Contaminants From Unmapped DNA and RNA in Pigs and Chickens Under Different Housing Conditions

Unmapped sequencing reads in livestock often contain valuable information about pathogens but are typically discarded. We analyzed blood-derived DNA and RNA from chickens and pigs kept under high- and low-biosecurity conditions, focusing on unmapped reads. In chickens, low-biosecurity farms harbored substantially more viral sequences, primarily plant viruses, indicating environmental contamination. In pigs, Mycoplasmoides pneumoniae and several pig-specific viruses were detected. Our bioinformatics pipeline, involving host read removal, assembly, BLAST, and taxonomic filtering, efficiently identified candidate pathogens and contaminants. This approach demonstrates the potential of sequencing-based environmental DNA monitoring to track microbial and viral presence, assess farm biosecurity, and support animal health surveillance.