Biology subjects

Geoghegan, J. L.

Publications and source records attributed to Geoghegan, J. L..

At least 19 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

Life-history and connectivity shape the viromes of a migratory and river-resident galaxiid

Migration can increase population connectivity and gene flow but may also facilitate pathogen transmission among hosts and habitats. The way life-history strategies shape viral diversity in closely related freshwater fishes remains poorly understood. Here, we used metatranscriptomics to compare the viromes of two fish in the family Galaxiidae with contrasting life-history strategies: amphidromous [i]nanga (Galaxias maculatus) and river-resident Gollum galaxias (Galaxias gollumoides). We analysed 54 pooled libraries derived from 416 individuals collected across 27 sites spanning multiple catchments and fish-passage barriers in southern New Zealand. A total of 13 novel fish-associated viruses were identified from five viral families (Astroviridae, Circoviridae, Coronaviridae, Hepeviridae, and Picornaviridae). Virome composition differed markedly between species, with only a single virus-positive pool detected among [i]nanga, whereas Gollum galaxias harboured 11 novel viruses, with circoviruses dominating the virome. No fish-associated viruses were detected in post-larval juveniles of either species, and alpha diversity did not differ significantly among catchments, sites or positions relative to fish-passage barriers. However, beta diversity analyses revealed significant spatial structuring of viral communities among sites and catchments, indicating localised variation in virome composition. Contrary to our predictions, the migratory species exhibited substantially lower viral diversity than the river-resident species. The absence of detectable viruses in juveniles, combined with the greater viral richness of the longer-lived Gollum galaxias, suggests that host longevity and cumulative environmental exposure may be important drivers of virome assembly. These findings demonstrate that host life-history strategy influences virome composition and reveal unexpectedly low viral diversity in a globally widespread migratory galaxiid, providing new insights into virus-host ecology and connectivity in freshwater fishes.

ecology↗

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

Disease investigation in a New Zealand high-health pig herd reveals a divergent porcine adenovirus

Porcine adenoviruses are common in domestic pigs and are generally regarded as low-pathogenicity viruses associated with mild or subclinical infections. However, their diversity, host associations and disease potential remain poorly understood. Here, we investigated a disease outbreak in an immunologically naive 320-sow high-health hysterectomy-derived pig herd in New Zealand. The outbreak was characterised by anorexia, lethargy, diffuse cutaneous erythema, death in neonatal piglets, and an increased occurrence of mummified fetuses. Histopathological examination of a piglet revealed widespread intranuclear inclusion bodies within endothelial cells, indicative of systemic viral infection. Total RNA sequencing was performed on tissues from an affected piglet and mummified fetuses. Metatranscriptomic analysis identified an abundant adenovirus in multiple piglet and aborted fetus tissues, and de novo assembly recovered a 27,685-nucleotide genome. Phylogenetic analysis placed the virus within the genus Mastadenovirus but it formed a divergent lineage distinct from all previously characterised porcine adenoviruses. Despite sequence divergence, the genome retained the characteristic organisation of mastadenoviruses. Aside from a single detection of porcine kobuvirus identified at low abundance in the small intestine and colon from the piglet, no other viral pathogens were identified. The high viral abundance and systemic tissue distribution observed in both the piglet and fetus, together with the presence of widespread adenoviral inclusion bodies in the piglet, support an association between this novel adenovirus and the disease outbreak. These findings expand the diversity of porcine adenoviruses and suggest that previously unrecognised adenovirus lineages may contribute to reproductive and neonatal disease when introduced into immunologically naive high-health herds.

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

Co-infections and cryptic pathogens uncovered by metatranscriptomics in New Zealands severe acute respiratory infections

Severe acute respiratory infections (SARI) are a leading cause of hospitalisation and mortality globally. Many SARI cases remain undiagnosed because kit-based PCR diagnostic panels are typically limited to one or a small number of known pathogens and may fail to identify low-abundance infections or novel, poorly characterised organisms. Here, we used metatranscriptomic sequencing to profile the total infectome of 300 PCR-negative SARI nasopharyngeal samples collected through sentinel hospital-based surveillance in New Zealand between 2014-2021. Our analysis revealed actively transcribing potential pathogens in 43% of SARI cases, comprising 10 RNA viruses, three DNA viruses, nine bacterial species and four fungal species. Notably, co-infections occurred in 26% of cases, revealing polymicrobial infections missed by routine diagnostics. Human rhinoviruses were the most frequently identified, despite not being detected by PCR, and multiple common-cold coronaviruses, human parechovirus A1 and parainfluenza virus type 4, were identified, although these were not included in the PCR screening panel. We also detected a range of bacterial and fungal species and uncovered highly expressed virulence and antimicrobial resistance genes. Infectome composition and diversity were shaped by key demographic and epidemiological factors, with strongest effects observed for age and year of sample collection, indicating that host characteristics and temporal dynamics influence both microbial richness and community structure. These findings highlight the limitations of current diagnostic strategies and the value of metatranscriptomics for comprehensive microbial identification. Integrating such genomic approaches into both clinical and public health frameworks could improve diagnostic accuracy, enabling more sensitive detection and characterisation of potential pathogens while also strengthening surveillance and outbreak response.

genomics↗

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

Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome

Yellow-eyed penguins (hoiho/takaraka, Megadyptes antipodes) are among the worlds rarest penguins and are regarded as a taonga (treasured) species in Aotearoa New Zealand. Since 2019, chicks on the New Zealand mainland have been affected by a deadly neonatal disease called respiratory distress syndrome (RDS), contributing to a decline to fewer than 143 breeding pairs. To investigate the putative genetic basis of this disease, we generated high-quality whole-genome data from 249 individuals spanning the species range, including from the New Zealand mainland (Northern range) and subantarctic Enderby and Campbell Islands (Southern). Population genomic analyses unexpectedly revealed three deeply divergent lineages with negligible gene flow, consistent with recognition of three distinct subspecies. Phylogenetic divergence dating suggests that these splits predate human arrival by several millennia, with the Northern lineage diverging from the Southern populations 5-16 ka. Genome scans for local adaptation revealed regions of strong differentiation, and genome-wide association analyses identified candidate immune and respiratory genes linked to RDS. In partnership with Ng[a]i Tahu, who hold indigenous guardianship over yellow-eyed penguins, we recommend recognition of three subspecies, urgent conservation action for the critically small and rapidly declining Northern subspecies, and the need for immediate population size and trend assessments for Auckland and Campbell Island populations.

genomics↗

bioRxiv2025

Evaluating sampling strategies for the detection of avian influenza viruses in the environment

Highly pathogenic avian influenza (HPAI) viruses threaten humans, livestock and wildlife, highlighting the urgent need for early warning surveillance. Environmental RNA (eRNA) monitoring provides a safer, cost-effective and non-invasive alternative to direct pathogen testing, yet the effectiveness of different sample types for avian influenza viruses (AIVs) is unclear. We evaluated four eRNA-based sampling methods in urban waterfowl ponds over approximately one year. All methods combined with RT-qPCR and metagenomic sequencing detected AIV, but detections were asynchronous, likely reflecting low viral concentrations or detection limits. These results highlight both the promise and the current limitations of eRNA-based AIV surveillance. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/677014v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@e8e189org.highwire.dtl.DTLVardef@12f17fforg.highwire.dtl.DTLVardef@d09f5forg.highwire.dtl.DTLVardef@8f55fd_HPS_FORMAT_FIGEXP M_FIG C_FIG

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↗

bioRxiv2025

Adaptations of DNA viruses are influenced by host and environment with proliferations constrained by environmental niche

Viruses are ubiquitous albeit individually constrained by host-range. Less well understood are environmental limitations on virus proliferation. To investigate estuarine viral diversity, niche constraints, and genomic traits of environmental adaptation, we analysed metagenomic and metatranscriptomic data from across an estuarine salinity gradient, including water and sediment habitats. We then expanded our analysis to globally distributed viral genomes. Viral distributions varied by estuary habitat, reflecting prokaryote community patterns, and highlighting that virus-host interactions are strongly influenced by environment. Viral lineages, up until approximately the rank of genus, were largely partitioned by ecological niche based on factors such as salinity and the aquatic-terrestrial divide. Across habitat boundaries, we identified variations in genomic GC content, and genomic signatures of salinity adaptation, particularly in virus major tail and capsid proteins. These included elevated ratios of acidic to basic amino acids and decreased protein isoelectric points at higher salinities which did not solely reflect biases inherited due to reliance on host machinery. Salinity is a well-described physiological stressor for prokaryotes. Results suggest that viruses employ some of the same osmoadaptive strategies independent of adaptation based on host machinery. Our findings indicate that, in addition to host range limitations, successful proliferation of viruses into distinct biomes (e.g. freshwater, saline, terrestrial) is constrained by adaptation to specific ecological niches.

microbiology↗

bioRxiv2025

A novel crustavirus associated with tail fan necrosis in New Zealand red rock lobsters, Jasus edwardsii

Tail fan necrosis (TFN) is a shell disease affecting spiny lobsters outer integument, with significant implications for the health and commercial viability of red rock lobsters (Jasus edwardsii) in New Zealand. Despite its impact, the potential role of a microbial agent in TFN remains poorly understood. Here, we conducted metatranscriptomic analyses on matching uropod and haemolymph samples from 15 red rock lobsters exhibiting TFN symptoms to characterise the associated microbial communities and search for putative candidates for further investigation. We report the discovery of a novel crustavirus (family: Nyamiviridae), named Red rock lobster crustavirus (RRLCV), consistently present in the uropod tissues of all sampled lobsters with TFN. RRLCVs presence and high abundance in uropod tissues suggest a potential association with TFN, although we found no direct relationship between viral abundance and TFN severity metrics, such as tissue loss. We also identified 30 bacterial genera across uropod samples, including previously associated groups, however, these were detected inconsistently. Our findings raise new questions about the tissue tropism, transmission, and potential pathogenicity of RRLCV in red rock lobsters. While TFN appears to be a multifactorial condition, RRLCV represents a promising candidate for further research into its role in the development of this disease.

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

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↗

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↗

bioRxiv2024

Viromes of Antarctic fish resembles the diversity found at lower latitudes

Antarctica harbours some of the most isolated and extreme environments on Earth, concealing a largely unexplored and unique component of the global animal virosphere. To understand the diversity and evolutionary histories of viruses in these polar species we determined the viromes of 11 Antarctic fish species with 248 samples collected from the Ross Sea region spanning the Perciformes, Gadiformes, and Scorpaeniformes orders. The continents shift southward and cooling temperatures over 20 million years ago led to a reduction in biodiversity and subsequent radiation of some marine fauna, such as the notothenioid fishes. Despite decreased host species richness in polar regions, we revealed a surprisingly complex virome diversity in Ross Sea fish, with the types and numbers of viruses per host species and individuals sampled comparable to that of fish in warmer marine environments with higher host community diversity. We also observed a higher number of closely related viruses likely representing instances of recent and historic host-switching events among Perciformes (all notothenioids) than in the Gadiformes, suggesting that rapid speciation events within this order generated closely related host species with few genetic barriers to cross-species transmission. Additionally, we identified novel genomic variation in an arenavirus with a split nucleoprotein sequence containing a stable helical structure, indicating potential adaptation of viral proteins to extreme temperatures. These findings enhance our understanding of virus evolution and virus-host interactions in response to environmental shifts, especially in less diverse ecosystems more vulnerable to the impacts of anthropogenic and climate changes.

microbiology↗

bioRxiv2024

Limited transmission of microbial species among coral reef fishes from the Great Barrier Reef, Australia

Reef fishes account for one-third of all extant marine fishes and exhibit enormous biodiversity within a highly interactive ecosystem. Yet relatively little is known about the diversity and evolution of microbial species (bacteria, viruses, and eukaryotes) associated with reef fish, even though this may provide valuable insights into the factors that shape microbial communities within vertebrate hosts as well as the extent and pattern of cross-species transmission. Through metatranscriptomic sequencing we characterised the viruses, bacteria, and single-celled eukaryotes from 128 reef fish species inhabiting Lizard Island and Orpheus Island on the Great Barrier Reef, Australia. We assessed whether microbial communities differed between islands that are separated by approximately 450 kilometres, and to what extent viruses were able to emerge in new hosts. Notably, despite strong ecological interactions in the reef environment, and the presence of the same families and subfamilies of viruses and bacteria on both islands, there was minimal evidence for the cross-species transmission of individual microorganisms among fish species. An exception was the high prevalence of the bacterial pathogen Photobacterium damselae among apparently healthy cardinalfishes from both islands, indicating that these fish species are natural reservoirs within the reef system. Overall, these data suggest that reef fishes have microbial-host associations that arose prior to the formation of the Great Barrier Reef, leading to strong host barriers to cross-species microbial transmission even within a highly interactive and species-rich environment.

microbiology↗

bioRxiv2023

Total infectome investigation of diphtheritic stomatitis in yellow-eyed penguins (Megadyptes antipodes) reveals a novel and abundant megrivirus

First identified in 2002, diphtheritic stomatitis (DS) is a devastating disease affecting yellow-eyed penguins (Megadyptes antipodes, or hoiho in te reo M[a]ori). The disease is associated with oral lesions in chicks and has caused significant morbidity and mortality. DS is widespread among yellow-eyed penguin chicks on mainland New Zealand yet appears to be absent from the subantarctic population. Corynebacterium spp. have previously been suspected as a causative agent yet, due to inconsistent cultures and inconclusive pathogenicity, its role in DS is unclear. Herein, we used a metatranscriptomic approach to identify potential causative agents of DS by revealing the presence and abundance of all viruses, bacteria, fungi and protozoa - together, the infectome. Oral and cloacal swab samples were collected from presymptomatic, symptomatic and recovered chicks along with a control group of healthy adults. Two novel viruses from the Picornaviridae were identified, one of which - yellow-eyed penguin megrivirus - was highly abundant in chicks irrespective of health status but not detected in healthy adults. Tissue from biopsied oral lesions also tested positive for the novel megrivirus upon PCR. We found no overall clustering among bacteria, protozoa and fungi communities at the genus level across samples, although Paraclostridium bifermentans was significantly more abundant in oral microbiota of symptomatic chicks compared to other groups. The detection of a novel and highly abundant megrivirus has sparked a new line of enquiry to investigate its potential association with DS.

microbiology↗