A large mortality event in New Zealand fur seals (Arctocephalus forsteri) caused by a divergent canine distemper virus

New Zealand is home to two species of resident otariids, the New Zealand fur seal (Arctocephalus forsteri, NZFS) and the endemic, endangered New Zealand sea lion (Phocarctos hookeri, NZSL), both of which were historically reduced to near extinction by commercial harvesting. While NZFS populations have shown signs of recovery, the NZSL remains endangered, with an estimated population of 10,000-12,000 and limited connectivity between subpopulations. Between May and June 2025, increased NZFS pup mortalities were observed at three colonies in New Zealand, prompting a multi-agency disease investigation led by the Ministry for Primary Industries. Avian influenza was rapidly excluded as the cause of these deaths via laboratory testing. A comprehensive diagnostic investigation including gross necropsy, histopathology, immunohistochemistry, and molecular assays identified a divergent strain of canine distemper virus (Morbillivirus canis, CDV) as the cause of death in 10/12 examined pups. Amplicon sequencing confirmed that the virus was near-identical to one detected at one of the affected colonies in 2024, and in archived samples from a separate, nearby site in 2020, indicating long-term circulation rather than a recent introduction. Although morbilliviruses have caused several mortality events in Northern Hemisphere phocids, this study provides the first definitive evidence of fatal morbillivirus infection in an otariid species and indicates that a divergent canine distemper virus may be endemic in NZFS populations. The potential threat to the endangered and sympatric NZSL is unclear and warrants further research.