Metatranscriptomic insights into the diversity, evolution and ecology of viruses in endemic and introduced passerines

Wild birds represent important yet under-studied viral reservoirs, harbouring potential pathogens that can impact both wildlife and human health. Their distinctive immune systems enable them to carry multiple infections without symptoms, while their mobility facilitates viral spread across species and ecosystems. Despite this, the factors shaping viral diversity in birds, and the extent of cross-species transmission, remain poorly understood, particularly in a New Zealand context.

This thesis investigated the virome, that is, the complete viral community within an individual, of endemic and introduced passerines in Aotearoa New Zealand within a spatially restricted ecological niche with shared water and food sources. We aimed to identify the drivers of viral diversity and potential for cross-species virus transmission. Using a metatranscriptomic approach, 443 birds were sampled over four years, and viral genomes were assembled to reconstruct their evolutionary histories. In total, 69 viral species spanning 14 families were identified, including 54 previously undescribed, novel viruses. Many of these viruses were closely related to viruses reported from birds in Asia, North America, Europe and Australia, highlighting both the paucity of knowledge about passerine viruses in New Zealand and the frequency of viral introductions via migratory birds, historic species translocations or cross-species transmission events.

We found that introduced passerines exhibited greater virome diversity than endemic species, and social behaviour emerged as a key driver, with flocking species harbouring higher viral richness and diversity than solitary or pair-living taxa. These findings provide critical insights into the ecological and behavioural determinants of viral diversity in passerines and establish a valuable baseline for health monitoring. In the context of emerging threats, such as highly pathogenic avian influenza virus, this work has important implications for disease surveillance, biosecurity, and avian conservation.