Biology subjects

Darnley, J. A.

Publications and source records attributed to Darnley, J. A..

4 recordsLinked to original sources

bioRxiv2026

Divergent coronaviruses discovered in the virome of lamprey with reddening syndrome

Lamprey reddening syndrome (LRS) is an emerging disease affecting pouched lamprey (Geotria australis; kanakana/piharau), a culturally and ecologically significant species in Aotearoa New Zealand. Characterised by skin haemorrhaging and elevated mortality, the aetiology of LRS has remained unresolved despite previous investigations. We used a metatranscriptomic approach to characterise viral communities in 28 lamprey from New Zealand and Tasmania, Australia, comparing diseased and presumably healthy individuals. This analysis revealed eight fish-infecting RNA viruses, seven of which were novel, including two highly divergent coronaviruses. One of these coronaviruses possessed a bi-segmented genome structure, and three lamprey were co-infected with both coronaviruses. While these coronaviruses were detected in both healthy and diseased individuals, lamprey with reddening exhibited markedly higher viral abundance, driven by elevated RNA transcripts of both viruses. This pattern suggests that increased coronavirus replication in diseased individuals may be influenced by host stress to environmental factors or co-infection with other pathogens, rather than acting as a sole causative agent of disease. Beyond identifying candidate viral associations, this study expands the known virosphere of an ancient vertebrate lineage and demonstrates the utility of genomics-informed diagnostics for investigating disease in threatened wildlife.

microbiology↗

bioRxiv2025

Foraging ecology drives viral community structure in New Zealand's aquatic birds

Wild migratory birds play a major role in the global spread of viruses, yet the diversity, host range and transmission patterns of viruses harboured by migratory species in Aotearoa/New Zealand remain largely unknown. This knowledge gap is critical given New Zealands position along major migratory flyways spanning Oceania, Antarctica and east Asia, where understanding viral diversity is key to assessing the risk of viral introductions such as highly pathogenic avian influenza virus and viral dispersal across these regions. To address this, we conducted the first large-scale metatranscriptomic survey of wild birds from New Zealand and its subantarctic islands, collecting 1,348 samples from 31 host species spanning four avian orders. We identified 118 avian viruses from 17 families, including 107 novel species, greatly expanding our knowledge of avian viral diversity. Viral communities differed significantly by host order and foraging behaviour, with scavenger birds harbouring more diverse viromes than non-scavengers. Although no HPAI subtypes were detected, we recovered a low-pathogenic avian influenza A/H1N9 virus from red knots (Calidris canutus) and a divergent tobanivirus from Auckland Island teal (Anas aucklandica), the first putative avian member of the Tobaniviridae. Notably, we detected 12 mammalian-associated viruses, primarily in scavenger birds, including Hedgehog hepatovirus, Rabbit haemorrhagic disease virus 2, and sea lion astroviruses, with mammalian host reads confirming their dietary origin. This study establishes the first virome baseline for New Zealands migratory birds, highlighting the ecological role of foraging in shaping viral communities and improving regional preparedness for HPAI and other emerging avian pathogens.

microbiology↗

bioRxiv2024

Oral and faecal viromes of New Zealand calves on pasture with an idiopathic ill-thrift syndrome

Since 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 symptomatic calves. Our analysis identified 18 bovine-associated viruses across two DNA and three RNA viral families, including five novel species. Oral viromes were dominated by Pseudocowpox virus, 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 in the calves complicates identifying 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.

microbiology↗

bioRxiv2024

Avian influenza virus surveillance across New Zealand and its subantarctic islands detects H1N9 in migratory shorebirds, but not 2.3.4.4b HPAI H5N1

Highly pathogenic avian influenza (HPAI) virus has never been detected in New Zealand. The potential impact of this virus on New Zealands wild birds would be catastrophic. To expand our knowledge of avian influenza viruses across New Zealand, we sampled wild aquatic birds from New Zealand, its outer islands and its subantarctic territories. Metatranscriptomic analysis of 700 individuals spanning 33 species revealed no detection of HPAI during the annual 2023-2024 migration. A single detection of H1N9 in red knots (Calidris canutus) was noted. This study provides a baseline for expanding avian influenza virus monitoring in New Zealand.

microbiology↗