Uncovering the faecal virome of New Zealand sea lions (Phocarctos hookeri) reveals virus sharing among geographically distinct pinnipeds

The New Zealand sea lion (pakake; Phocarctos hookeri) is the largest and only endemic otariid species in Aotearoa (New Zealand), classified as ‘nationally critical’ due to low population numbers and limited distribution. Infectious disease is a significant factor contributing to sea lion population instability; however, we know almost nothing about viral organisms harboured by these species. To this end, we conducted a metatranscriptomic analysis of faecal samples from healthy New Zealand sea lions collected along the Otago coastline over twelve months. In total, we identified 11 viral species, eight of which were novel, spanning four RNA viral families, including virus species also found in California sea lions suggesting sustained viral sharing among these geographically distinct marine mammals. Our analysis also revealed that virome community composition was not altered by ecological factors such as host sex, age and migratory status. This study lays the groundwork for future research on marine mammal viromes, with important implications for disease monitoring and conservation efforts, particularly in the wake of highly pathogenic avian influenza virus.