Biology subjects

Van Brussel, K.

Publications and source records attributed to Van Brussel, K..

8 recordsLinked to original sources

bioRxiv2025

Viral diversity, ecological interconnectedness, and the identification of mammalian chuviruses in Australian microbats

Microbats are a large and ecologically important group of Australian mammalian fauna. However, their RNA virome diversity, as well as its ecological and evolutionary significance, has received limited study. We applied a metatranscriptomic approach to reveal more of the diversity of RNA viruses present in faeces from different microbat species in New South Wales and South Australia, including the critically endangered Southern bent-wing bat (Miniopterus schreibersii bassanii) from the Naracoorte bat maternity caves in South Australia. The data generated revealed a high diversity of RNA viruses, including 51 likely mammalian-associated viruses classified into ten taxonomic groups, including the Coronaviridae, Hepeviridae and Chuviridae. Notably, we identified a mammalian-specific lineage of chuviruses associated with bats in Australia and of bats and rodents in China, strongly suggesting that viruses of this family have established sustained transmission cycles in mammals as well as invertebrates. Our results also revealed widespread viral connectivity among alphacoronaviruses across multiple microbat species in mainland Australia and Christmas Island, indicative of long distance viral movement. High viral diversity and virus co-circulation was observed within the Southern bent-wing bat population of the Naracoorte caves, suggesting complex population dynamics that might facilitate virus maintenance and transmission. Overall, these findings highlight the role of Australian microbats as viral reservoirs, including the presence of viruses not previously associated with sustained mammalian transmission.

microbiology↗

bioRxiv2025

Limited effect of short- to mid-term storage conditions on an Australian farmland soil RNA virome

Soils represent one of the largest and most diverse reservoirs of microbial life on Earth, yet their associated RNA viruses remain underexplored compared to animal and aquatic systems. Viral discovery in soils has been further limited by technical hurdles, particularly obtaining sufficient yields of high-quality RNA for sequencing. To address this, we evaluated a range of storage and preservation strategies, including the use of commercial preservative solutions and ultra-cold snap-freezing, followed by standardised RNA extraction, sequencing, and virus discovery pipelines. This work aimed to establish minimum sample storage requirements that maintain RNA integrity, generate sufficient RNA sequencing data, and subsequently enable reliable soil virome characterisation. While no preservative solution proved effective, "neat" soil samples were stable at 2-8{degrees}C and -30{degrees}C for at least two weeks, and at -80{degrees}C for at least three months, with no measurable reduction in RNA quality, sequencing data, or viral abundance and diversity. From 32 resulting sequencing libraries, we identified 1,475 putative novel RNA viruses, with the majority belonging to the microbe-associated phylum Lenarviricota. Several novel viruses formed divergent clusters with other environmentally derived sequences distantly related to traditionally animal-associated families such as the Astroviridae and Picornaviridae. Furthermore, unique clusters within the Picobirnaviridae, Alsuvurucetes, Ghabrivirales, and Amabiliviricetes comprised exclusively Australian viruses, suggesting instances of region-specific evolution. Together, these findings highlight soils as rich reservoirs of RNA viral diversity and provide practical minimum standards for storage, expanding opportunities to investigate the ecological and evolutionary roles of RNA viruses in terrestrial systems. ImportanceRNA viruses are the most abundant and diverse biological entities on Earth and are likely present in all other organisms and ecosystems, including soil-dwelling invertebrates, microbes, and plants. Despite this, their diversity and role in soil systems remains largely unknown. Methodological challenges in preserving and extracting sufficient quantities of RNA from soils have hindered the study of these communities. Here, we identified 1,475 previously undescribed RNA viruses in Australian soils while systematically testing different preservation strategies. The significance of our research lies in the demonstration that snap-freezing soil is a viable and robust storage strategy for at least three months, while also highlighting the extraordinary scale of viral diversity present in terrestrial environments. This work establishes a foundation for reliable exploration of terrestrial RNA viruses, improving the accessibility of more remote environmental viromes and enabling future efforts to integrate them into broader models of microbial ecology and ecosystem function.

microbiology↗

bioRxiv2025

Diverse Viral Pathogens in Australian Canines: Limited Geographic Structure and the First Detection of an RNA Virus in Dingoes

Viruses impose a substantial disease burden on dogs and the close relationship between dogs and humans may facilitate zoonotic disease emergence. Australias geographic isolation, strict biosecurity measures and native dingo populations present a unique model for understanding the spread and evolution of canine viruses. However, aside from a few well-characterised pathogens, genomic data are scarce for many common dog viruses, limiting our understanding of their evolution and disease ecology. Using a metatranscriptomic approach we identified the viruses in dogs and dingoes from various geographical locations across mainland Australia and sample types, revealing 86 vertebrate-associated viruses belonging to 16 distinct species, including a new vesivirus-like species. Many of the viruses identified here have not previously been sequenced in Australia. We identified important dog pathogens associated with canine infectious respiratory disease syndrome--such as canine pneumovirus, canine herpesvirus, and canine respiratory coronavirus--and gastroenteritis, including canine parvovirus, canine coronavirus, and rotavirus A. The sequences of Australian canine viruses often occupied multiple distinct clades phylogenetically and had little geographic structure, suggesting multiple virus introductions and subsequent spread across the country. Notably, we identified the first RNA virus - rotavirus A - in a dingo. This virus was phylogenetically distinct from dog-associated rotavirus A sequences and more closely related to viruses found in humans and bats, indicative of the past cross-species transmission of a reassortant virus into dingoes, and shows dingoes and domestic dogs may have distinct viromes. Our findings expand the knowledge of viral diversity in Australian canines, improving our understanding of viral movement into and within Australia, as well as the potential zoonotic risks associated with dogs and dingoes.

microbiology↗

bioRxiv2024

Tunicate metatranscriptomes reveal ancient virus-host co-divergence and inter-order recombination in the evolutionary history of disease-causing viruses

Tunicates are a key transitional taxon in animal evolution as the closest extant invertebrate relatives of the vertebrates. Their viruses may also reflect this transitional state. Yet, it is not known whether tunicate viruses are more closely related to vertebrate- or invertebrate-infecting viral lineages. We analysed primary and publicly available RNA libraries to extend the known diversity of tunicate-associated viruses and determine their relationship to viruses of other animals. We present evidence that influenza viruses, alphaviruses, and some mononegaviruses emerged prior to the evolution of vertebrates. We also show that the recombination of glycoproteins between different orders of RNA viruses, including between positive- and negative-sense viruses, may have shaped the evolution of multiple lineages. Our study reveals that some disease-causing RNA virus lineages were present in early chordates and highlights that the evolution of structural genes may be incongruent with that of the highly conserved RNA-dependent RNA polymerase.

microbiology↗

bioRxiv2024

Detection of exotic biosecurity threat ribgrass mosaic virus and novel tobamoviruses through metatranscriptomic sequencing of animal gut content

Ribgrass mosaic virus (RMV) and related viruses of the genus Tobamovirus (Virgaviridae) are cruciferous plant pathogens that represent a threat to global horticultural systems. In Australia, they are considered exotic biosecurity threats, and an incursion of these viruses would require rapid and strict control efforts. However, current surveillance methods for these viruses are limited. We examined whether RMV and related tobamoviruses could be detected by deep sequencing of gut metatranscriptomes of vertebrate animals and ticks. Using this method, we discovered that RMV, as well as a novel relative of RMV, and two highly diverse novel tobamoviruses are present in Australia. RMV was detected in multiple sites in both the Australian Capital Territory (ACT) and Tasmania, two regions separated by approximately 700km of land and 200km of water. The novel relative of RMV was detected in the ACT and New South Wales (NSW), while the highly divergent novel tobamoviruses were each detected in a single state, NSW and Queensland (QLD). In addition, Tobacco mild green mosaic virus, which is already known to be present in Australia, was detected in QLD using this method. This work highlights the potential utility of metatranscriptomic sequencing of wild animal gut for the surveillance of biosecurity threats to native and agricultural plant species. ImportancePlant viruses can have devastating impacts on global horticulture. Tobamoviruses (family Virgaviridae, genus Tobamovirus) are among the most damaging seed-borne viruses in horticultural crops, and Australia is free of many of the tobamoviruses that cause major crop losses in other countries. These viruses are extremely difficult to eradicate. Consequently, early detection of incursions is key to the control of these viruses in Australia, alongside rapid deployment of eradication and management plans. Current biosecurity surveillance methods in Australia rely on visual inspection, immunological assays, and molecular methods such as screening of imported seed lots. This study introduces a complementary approach that utilises unbiased metatranscriptomic sequencing of animal gut material to detect cryptic plant viruses circulating in nature. Using this approach, we detected five different tobamovirus circulating in Australia, including a virus thought to be exotic and three novel viruses. This unique approach highlights alternative options for surveillance/detection of exotic crop viruses.

microbiology↗

bioRxiv2023

Identification of a novel papillomavirus from a New Zealand fur seal (Arctocephalus forsteri) with oral papilloma-like lesions

Despite being the predominant seal species in the Australian-New Zealand region and serving as a key indicator of marine environmental health, little is known about infectious diseases in New Zealand fur seals (Long-nosed fur seal; Arctocephalus forsteri). Several papillomaviruses have been identified in earless seals and sea lions, with the latter linked to cutaneous plaques and invasive squamous cell carcinoma. To date, no papillomaviruses have been reported in fur seals. We used traditional veterinary diagnostic techniques and metatranscriptomic sequencing of tissue samples to investigate the virome of New Zealand fur seals. We identified a novel papillomavirus, provisionally termed Arctocephalus forsteri papillomavirus 1 (AfPV1) in an animal with clinically and histologically identified oral papilloma-like lesions. RT-PCR confirmed the presence of AfPV1 only in oral papilloma samples from the affected individual. Phylogenetic analysis of the complete 7,926 bp genome of AfPV1 revealed that it clustered with taupapillomaviruses found in related Carnivora species. In addition, we identified the partial genome of a novel Gammaherpesvirus, Arctocephalus forsteri gammaherpesvirus 1 (AfGHV1), in a different individual without pathological evidence of viral infection. These findings highlight the need for further research into the disease associations and impact of undiagnosed and novel viruses on New Zealand fur seals.

microbiology↗

bioRxiv2023

Evidence for an aquatic origin of influenza virus and the order Articulavirales

The emergence of novel disease-causing viruses in mammals is part of the long evolutionary history of viruses. Tracing these evolutionary histories contextualises virus spill over events and may help to elucidate how and why they occur. We used a combination of total RNA sequencing and transcriptome data mining to extend the diversity and evolutionary history of the order Articulavirales, which includes the influenza viruses. From this, we identified the first instance of Articulavirales in the Cnidaria (including corals), constituting a novel and divergent family that we tentatively named the Cnidenomoviridae. This may be the basal group within the Articulavirales. We also extended the known evolutionary history of the influenza virus lineage by identifying a highly divergent, sturgeon-associated influenza virus. This suggests that fish were among the first hosts of influenza viruses. Finally, we substantially expanded the known diversity of quaranjaviruses and proposed that this genus be reclassified as a family (the Quaranjaviridae). We find evidence that vertebrate infecting Quaranjaviridae may have initially evolved in crustaceans before spilling into terrestrial Chelicerata (i.e., ticks). Together, our findings indicate that the Articulavirales has evolved over at least 600 million years, first emerging in aquatic animals. Importantly, the evolution of this order was not shaped by strict virus-host codivergence, but rather by multiple aquatic-terrestrial transitions and substantial host jumps, some of which are still observable today.

evolutionary biology↗

bioRxiv2022

Gammaretroviruses, novel viruses and pathogenic bacteria in Australian bats with neurological signs, pneumonia and skin lesions

More than 70 bat species are found in mainland Australia, including five species of megabat from a single genus (family Pteropodidae) and more than 65 species representing six families of microbats. The conservation status of these animals varies from least concern to endangered. Research directed at evaluating the impact of microorganisms on bat health has been generally restricted to surveillance for specific pathogens. While most of the current bat virome studies focus on sampling apparently healthy individuals, little is known about the infectome of diseased bats. We performed traditional diagnostic techniques and metatranscriptomic sequencing on tissue samples from 43 individual bats, comprising three flying fox and two microbat species experiencing a range of disease syndromes, including mass mortality, neurological signs, pneumonia and skin lesions. We identified reads from four pathogenic bacteria and two pathogenic fungi, including Pseudomonas aeruginosa in lung samples from flying foxes with peracute pneumonia, and with dermatitis. Of note, we identified the recently discovered Hervey pteropid gammaretrovirus, with evidence of replication consistent with an exogenous virus, in a bat with lymphoid leukemia. In addition, one novel picornavirus, at least three novel astroviruses and bat pegiviruses were identified. We suggest that the most likely cause of peracute lung disease was Pseudomonas aeruginosa, while we suspect Hervey pteropid gammaretrovirus was associated with lymphoid leukemia. It is possible that any of the novel astroviruses could have contributed to the presentation of skin lesions in individual microbats. This study highlights the importance of studying the role of microorganisms in bat health and conservation. IMPORTANCEBats have been implicated as reservoir hosts for zoonotic disease of concern, however, the burden of microorganism including viruses on bat health and disease is understudied. Here we incorporated veterinary diagnostics and RNA sequencing to identify the presence of microbes and viruses with possible pathogenic status in Australian bats with varying disease presentations. These techniques were able to effectively identify and describe several pathogenic species of bacteria and fungi in addition to known and novel viruses. This study emphasises the importance of screening pathogens in cases of bat mortality for the conservation of this diverse order.

microbiology↗