Biology subjects

French, R. K.

Publications and source records attributed to French, R. K..

9 recordsLinked to original sources

bioRxiv2026

Social behaviour is a key determinant of virome diversity in New Zealand passerines

Wild birds are important reservoirs of viral diversity and can play key roles in the emergence and dispersal of infectious diseases. Their ability to harbour multiple infections without overt disease, combined with their mobility and ecological interactions, creates opportunities for viruses to spread across species and geographic regions. Despite this, the factors shaping avian viromes remain poorly understood, particularly in Aotearoa New Zealand, where endemic and introduced bird species coexist within a relatively isolated ecosystem. This study used metatranscriptomic sequencing to characterise the viromes of 443 endemic and introduced passerines sampled over four years within a shared ecological setting. A total of 217 viruses, representing 69 viral species across 14 families, were identified, including 54 previously undescribed viruses. Many were closely related to viruses reported from birds in Asia, North America, Europe and Australia, suggesting historical or ongoing viral exchange through migration, co-divergence or cross-species transmission. Introduced passerines harboured greater viral diversity than endemic species, while social behaviour was a key predictor of virome composition with flocking species exhibiting higher viral richness and diversity than solitary or pair-living taxa. In contrast, non-viral microbial communities were primarily shaped by host species and diet, indicating that viral communities are influenced by ecological processes distinct from those associated with the non-viral microbiome. These findings provide new insight into the ecological and behavioural drivers of avian viral diversity.

microbiology↗

bioRxiv2026

Urban waterfowl harbour geographically connected viral communities across Aotearoa New Zealand

Urban waterfowl are important natural reservoirs of viruses that can affect wildlife, livestock and human health, yet the diversity and spatial distribution of these viral communities remain poorly understood. Here, we characterised the faecal viromes of urban waterfowl sampled from 13 locations across the length of Aotearoa (New Zealand). We identified 96 avian viruses (50 species) spanning nine viral families, including 33 previously undescribed viruses. Picornaviruses were the most widespread viral group, while several viruses were closely related to those previously identified in Australian waterfowl, indicating that some viral lineages are likely distributed across the broader Australasian region. Despite sampling locations spanning more than 1,500 km, virome composition exhibited little evidence of geographic structure, with little difference in viral diversity or community composition between sampling locations. Network analyses similarly demonstrated extensive sharing of virus species among sampling locations, indicating little geographic structuring of virome composition among urban waterfowl. In addition, we recovered the complete genome of a low-pathogenic A(H3N8) influenza A virus from mallards (Anas platyrhynchos) in the most southern region of Aotearoa. These findings reveal extensive viral diversity and widespread connectivity among urban waterfowl, providing new insights into viral ecology and the potential for widespread virus distribution across Aotearoa.

microbiology↗

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↗

bioRxiv2026

The RNA virome of intertidal kelp in New Zealand reveals novel viral lineages associated with unhealthy kelp

Pathogens can have major impacts on ecosystem function, especially when they infect foundational taxa such as habitat-forming kelp. Understanding which potentially pathogenic microbes are in an ecosystem is increasingly important as environmental change intensifies ecosystem imbalances, yet few studies have examined which viruses are associated with key habitat-forming macroalgae. Here, we screened multiple populations of intertidal / shallow-subtidal macroalgae in New Zealand for viruses. Samples were collected from three southern bull kelp species: Durvillaea antarctica, Durvillaea poha and Durvillaea willana. Total RNA was extracted and sequenced from both obviously unhealthy kelp tissue and apparently healthy tissue. We identified several novel viruses belonging to the families Mitoviridae, Narnaviridae, Partitiviridae, Totiviridae, and the recently proposed Ormycovirus group. Viral abundance and diversity were notably higher at Lawyers Head (the site closest to a city) compared to other sites, especially in unhealthy kelp samples. The elevated viral presence at Lawyers Head may indicate that human impacts, such as pollution, are influencing viral prevalence. This study reveals that coastal macroalgae in New Zealand host diverse viral lineages, some likely pathogenic, and hints at the potential influence of anthropogenic pollution on marine virome composition.

microbiology↗

bioRxiv2025

Viral surveillance of invasive mammals in New Zealand reveals unique viral lineages reflecting their introduction history

Introduced mammalian species in Aotearoa New Zealand pose significant ecological risks and may serve as reservoirs for novel or emerging infectious diseases. In this study, we present the first metatranscriptomic survey of viruses in five introduced mammals: ferrets (Mustela furo), stoats (Mustela erminea), weasels (Mustela nivalis), brushtail possums (Trichosurus vulpecula), and European hedgehogs (Erinaceus europaeus), sampled across both the North and South Islands. Through total RNA sequencing, we identified 11 mammalian-infecting viruses spanning eight viral families, including four novel virus species: Ferret mastadenovirus, Possum astrovirus, Ferret pestivirus, and Weasel jeilongvirus. Whole genomes were recovered for six of these viruses, enabling detailed phylogenetic analysis. Notably, we observed strong global geographic clustering in both Wobbly possum disease virus and Ferret hepatitis E virus, suggesting localized viral evolution following the introduction of their hosts into New Zealand. In addition, the detection of Human rotavirus A in hedgehogs highlights the possibility of reverse zoonotic transmission. Together, these findings broaden our understanding of the viral diversity harboured by New Zealands introduced mammals and provide a critical foundation for future biocontrol and disease surveillance ehorts. IMPORTANCEIntroduced mammals in Aotearoa New Zealand not only threaten native biodiversity through predation and competition, but also represent a largely overlooked source of infectious disease risk. Viruses circulating in these species may spill over into native wildlife, livestock, or even humans, while human viruses can also establish in introduced animals and create new reservoirs. Understanding which viruses are present, and how they evolve in isolated host populations, is critical for anticipating future disease outbreaks, improving biosecurity, and guiding wildlife management strategies. This work provides foundational knowledge that links ecology, conservation, and health, highlighting the need to consider pathogens as part of the broader impact of invasive species.

microbiology↗

bioRxiv2024

Evidence for a role of extraintestinal pathogenic Escherichia coli, Enterococcus faecalis and Streptococcus gallolyticus in the aetiology of exudative cloacitis in the critically endangered kakapo (Strigops habroptilus)

The k[a]k[a]p[o] is a critically endangered flightless parrot which suffers from exudative cloacitis, a debilitating disease resulting in inflammation of the vent margin or cloaca. Despite this disease emerging over 20 years ago, the cause of exudative cloacitis remains elusive. We used total RNA sequencing and metatranscriptomic analysis to characterise the infectome of lesions and cloacal swabs from nine k[a]k[a]p[o] affected with exudative cloacitis, and compared this to cloacal swabs from 45 non-diseased k[a]k[a]p[o]. We identified three bacterial species - Streptococcus gallolyticus, Enterococcus faecalis and Escherichia coli - as significantly more abundant in diseased k[a]k[a]p[o] compared to healthy individuals. The genetic diversity observed in both S. gallolyticus and E. faecalis among diseased k[a]k[a]p[o] suggests that these bacteria originate from exogenous sources rather than from k[a]k[a]p[o]-to-k[a]k[a]p[o] transmission. The presence of extraintestinal pathogenic E. coli (ExPEC)-associated virulence factors in the diseased k[a]k[a]p[o] population suggests that E. coli may play a critical role in disease progression by facilitating iron acquisition and causing DNA damage in host cells, possibly in association with E. faecalis. No avian viral, fungal nor other parasitic species were identified. These results, combined with the consistent presence of one E. coli gnd sequence type across multiple diseased birds, suggests that this species may be the primary cause of exudative cloacitis. These findings shed light on possible causative agents of exudative cloacitis, and offer insights into the interplay of microbial factors influencing the disease.

microbiology↗

bioRxiv2022

Host Phylogeny Shapes Viral Transmission Networks in an Island Ecosystem

Viral transmission between host species underpins disease emergence. Both host phylogenetic relatedness and aspects of their ecology, such as species interactions and predator-prey relationships, may govern cross-species virus transmission and zoonotic risk, although their relative impact is unknown. By characterising the virome of a relatively isolated island ecological community linked through a food web we show that phylogenetic barriers result in distantly related host species sharing fewer viruses. Host ecology had a much smaller influence on overall virome composition. Network analysis revealed that hosts with a high diversity of viruses were more likely to gain new viruses, and that generalist viruses were more likely to infect new hosts. Such a highly connected ecological community heightens the risk of disease emergence, particularly among closely related species. One-Sentence SummarySequencing of an entire island virome reveals that closely related hosts have highly connected virus communities, increasing emergence risk.

microbiology↗

bioRxiv2022

Novel Viral and Microbial Species in a Translocated Toutouwai (Petroica longipes) Population from Aotearoa/New Zealand

BackgroundTranslocation is a common tool in wildlife management and been responsible for many conservation successes. During translocations, any associated infectious agents are moved with their wildlife hosts. Accordingly, translocations can present a risk of infectious disease emergence, although they also provide an opportunity to restore natural infectious communities ( infectome) and mitigate the long-term risks of reduced natural resistance. MethodsWe used metatranscriptomic sequencing to characterise the infectome of 41 toutouwai (North Island robin, Petroica longipes) that were translocated to establish a new population within the North Island of New Zealand. We also screened for pathogenic bacteria, fungi and parasites. ResultsAlthough we did not detect any known avian diseases, which is a positive outcome for the translocated toutouwai population, we identified a number of novel viruses of interest, including a novel avian hepatovirus, as well as a divergent calici-like virus and four hepe-like viruses of which the host species is unknown. We also revealed a novel spirochete bacterium and a coccidian eukaryotic parasite. ConclusionsThe presumably non-pathogenic viruses and microbial species identified here support the idea that the majority of microorganisms likely do not cause disease in their hosts, and that translocations could serve to help restore and maintain native infectious communities. We advise greater surveillance of infectious communities of both native and non-native wildlife before and after translocations to better understand the impact, positive or negative, that such movements may have on both host and infectome ecology.

microbiology↗

bioRxiv2022

Metatranscriptomic comparison of viromes in endemic and introduced passerines in New Zealand

New Zealand has many endemic passerine birds vulnerable to emerging infectious diseases. Yet little is known about viruses in passerines, and in some countries, including New Zealand, the virome of wild passerines has received little research attention. Using metatranscriptomic sequencing we characterised the virome of New Zealand endemic and introduced species of passerine. Accordingly, we identified 34 possible avian viruses from cloacal swabs of 12 endemic and introduced bird species not showing signs of disease. These included a novel siadenovirus, iltovirus and avastrovirus in the Eurasian blackbird (Turdus merula, an introduced species), song thrush (Turdus philomelos, introduced) and silvereye (Zosterops lateralis, introduced), respectively. This is the first time novel viruses from these genera have been identified in New Zealand, likely reflecting prior undersampling. It also represents the first identification of an iltovirus and siadenovirus in blackbirds and thrushes globally. These three viruses were found only in introduced species and may pose a risk to endemic species if they were to jump species boundaries, particularly the iltoviruses and siadenoviruses that have a prior history of disease associations. Further virus study and surveillance is needed in New Zealand avifauna, particularly in Turdus populations and endemic species.

bioinformatics↗