Grimwood RMDarnley JAO’Connell JPHunt HTaylor HSLawrence KEAbbott MBWJauregui RGeoghegan JLZhai S-L2025-08-202025-08-202025-07-28Grimwood RM, Darnley JA, O’Connell JP, Hunt H, Taylor HS, Lawrence KE, Abbott MBW, Jauregui R, Geoghegan JL. (2025). Oral and Faecal Viromes of New Zealand Calves on Pasture With an Idiopathic Ill-Thrift Syndrome. Transboundary and Emerging Diseases. 2025. 1.1865-1674https://mro.massey.ac.nz/handle/10179/73391Since 2015, an idiopathic ill-thrift syndrome featuring diarrhoea and, in some cases, gastrointestinal ulceration has been reported in weaned New Zealand dairy calves. Similar syndromes have been described in the British Isles and Australia, but investigations in New Zealand have yet to identify a specific cause. Notably, the viromes of affected calves remain understudied. We conducted metatranscriptomic analyses of oral and faecal viromes in 11 calves from a dairy farm in Taranaki, New Zealand, experiencing an outbreak of this syndrome. This included nine calves showing clinical signs. Our analysis identified 18 bovine-associated viruses across two DNA and three RNA viral families, including six novel species. Oral viromes were dominated by Pseudocowpox virus, which was detected in all calves with oral lesions. Faecal viromes were more diverse, featuring adenoviruses, caliciviruses, astroviruses and picornaviruses. Bovine bopivirus, from the Picornaviridae family and previously unreported in New Zealand, was significantly associated with calves showing oral lesions and diarrhoea, indicating a possible link to disease, though its role remains unclear. The diverse viral communities of the calves complicate the identification of a single causative agent. Importantly, no novel viruses were significantly associated with the syndrome, and the viromes closely resembled those found in cattle globally. These findings suggest the syndrome likely has a multifactorial origin involving nutritional, management and environmental factors rather than being driven primarily by known or novel viruses. Further, research across regions and seasons is recommended to clarify the role of viruses in idiopathic ill-thrift among New Zealand calves.(c) 2025 The Author/sCC BY 4.0https://creativecommons.org/licenses/by/4.0/Bovine bopiviruscalfenteritisidiopathic ill-thriftNew ZealandPseudocowpox virusstomatitisvirus discoveryJournal article10.1155/tbed/77379891865-1682journal-article737989