A5022062973- Influenza Virus Research Studies
- Viral Infections and Vectors
- Animal Disease Management and Epidemiology
- Animal Virus Infections Studies
- Respiratory viral infections research
- Viral gastroenteritis research and epidemiology
- Zoonotic diseases and public health
- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- Plant Virus Research Studies
- Environmental DNA in Biodiversity Studies
- Aquaculture disease management and microbiota
- Virology and Viral Diseases
- Microbial Community Ecology and Physiology
- Gut microbiota and health
- Avian ecology and behavior
- COVID-19 epidemiological studies
- interferon and immune responses
- Pharmaceutical and Antibiotic Environmental Impacts
- Hepatitis B Virus Studies
- Per- and polyfluoroalkyl substances research
- Virus-based gene therapy research
- Vibrio bacteria research studies
- Plant and Fungal Interactions Research
- Vector-Borne Animal Diseases
The University of Melbourne
2021-2025
Peter Doherty Institute
2017-2025
The University of Sydney
2020-2025
Taronga Conservation Society Australia
2021-2024
The Royal Melbourne Hospital
2023-2024
Uppsala University
2016-2023
Scientific Committee on Antarctic Research
2023
Linnaeus University
2012-2022
Cooperative Trials Group for Neuro-Oncology
2022
Engineering Service Center und Handel (Germany)
2020
Unprecedented outbreaks of the H5N1 highly pathogenic avian influenza virus raise concern.
Abstract Genomics is a cornerstone of modern pathogen epidemiology yet demonstrating transmission in One Health context challenging, as strains circulate and evolve within between diverse hosts environments. To identify phylogenetic linkages better define relevant measures genomic relatedness context, we collated 5471 Escherichia coli genome sequences from Australia originating humans ( n = 2996), wild animals 870), livestock 649), companion 375), environmental sources 292) food 289)...
Abstract There is an increasing demand for accurate and fast metagenome classifiers that can not only identify bacteria, but all members of a microbial community. We used recently developed concept in read mapping to develop highly metagenomic classification pipeline named CCMetagen. The substantially outperforms other commonly software identifying bacteria fungi efficiently use the entire NCBI nucleotide collection as reference detect species with incomplete genome data from biological...
Data on long-term circulation of pathogens in wildlife populations are seldom collected, and hence understanding spatial-temporal variation prevalence genotypes is limited. Here, we analysed a surveillance series influenza A virus (IAV) mallards collected at an important migratory stopover site from 2002 to 2010, characterized seasonal dynamics subtype diversity. Prevalence were influenced by year, but retained common pattern for all years whereby was low spring summer, increased early...
Antibiotic resistance is rendering common bacterial infections untreatable. Wildlife can incorporate and disperse antibiotic-resistant bacteria in the environment, such as water systems, which turn serve reservoirs of genes for human pathogens. Anthropogenic activity may contribute to spread cycling through natural environments, including release waste, sewage treatment only partially removes bacteria. However, empirical data supporting these effects are currently limited. Here we used bulk...
Little is known about the factors that shape ecology of RNA viruses in nature. Wild birds are an important case point, as other than influenza A virus, avian samples rarely tested for viruses, especially absence overt disease. Using bulk RNA-sequencing ("meta-transcriptomics"), we revealed viral diversity present Australian wild through lens ecological may determine virome structure and abundance. meta-transcriptomic analysis four Anseriformes (waterfowl) Charadriiformes (shorebird) species...
Abstract Revealing the determinants of virome composition is central to placing disease emergence in a broader evolutionary context. Fish are most species-rich group vertebrates and so provide an ideal model system study factors that shape compositions their evolution. We characterized viromes nineteen wild-caught species marine fish using total RNA sequencing (meta-transcriptomics) combined with analyses sequence protein structural homology identify divergent viruses often evade...
Hepatitis delta virus (HDV) is currently only found in humans and a satellite that depends on hepatitis B (HBV) envelope proteins for assembly, release, entry. Using meta-transcriptomics, we identified the genome of novel HDV-like agent ducks. Sequence analysis revealed secondary structures were shared with HDV, including self-complementarity ribozyme features. The predicted viral protein shares 32% amino acid similarity to small antigen HDV comprises divergent phylogenetic lineage....
Abstract Hepatitis delta virus (HDV) is the smallest known RNA virus, encoding a single protein. Until recently, HDV had only been identified in humans, where it strongly associated with co-infection hepatitis B (HBV). However, recent discovery of HDV-like viruses metagenomic samples from birds and snakes suggests that this has far longer evolutionary history. Herein, using additional meta-transcriptomic data, we show highly divergent are also present fish, amphibians, invertebrates, PCR...
Abstract Despite its isolation and extreme climate, Antarctica is home to diverse fauna associated microorganisms. It has been proposed that the most iconic Antarctic animal, penguin, experiences low pathogen pressure, accounting for their disease susceptibility in foreign environments. There is, however, a limited understanding of virome diversity species, extent situ virus evolution, or how it relates other geographic regions. To assess whether penguins have microbial we determined RNA...
Identifying the animal reservoirs from which zoonotic viruses will likely emerge is central to understanding determinants of disease emergence. Accordingly, there has been an increase in studies attempting “risk assessment.” Herein, we demonstrate that virological data on these analyses are conducted incomplete, biased, and rapidly changing with ongoing virus discovery. Together, shortcomings suggest attempts assess risk using available be inaccurate largely only identify those host taxa...
Host susceptibility to parasites is mediated by intrinsic and external factors such as genetics, ecology, age season. While waterfowl are considered central the reservoir community for low pathogenic avian influenza A viruses (LPAIV), role of host phylogeny has received limited formal attention. Herein, we analysed 12 339 oropharyngeal cloacal swabs 10 826 serum samples collected over 11 years from wild birds in Australia. As well describing species-level differences prevalence...
Abstract Virus transmission between host species underpins disease emergence. Both phylogenetic relatedness and aspects of their ecology, such as interactions predator–prey relationships, may govern rates patterns cross-species virus hence zoonotic risk. To address the impact phylogeny ecology on diversity evolution, we characterized virome structure a relatively isolated island ecological community in Fiordland, New Zealand, that are linked through food web. We show barriers inhibited...
Abstract Emerging infectious diseases are increasingly understood as a hallmark of the Anthropocene 1–3 . Most experts agree that anthropogenic ecosystem change and high-risk contact among people, livestock, wildlife have contributed to recent emergence new zoonotic, vector-borne, environmentally-transmitted pathogens 1,4–6 However, extent which these factors also structure landscapes human infection outbreak risk is not well understood, beyond certain well-studied disease systems 7–9 Here,...
Due to limited interaction of migratory birds between Eurasia and America, two independent avian influenza virus (AIV) gene pools have evolved. There is evidence low frequency reassortment these regions, which has major implications in global AIV dynamics. Indeed, all currently circulating lineages the PB1 PA segments North America are Eurasian origin. Large-scale analyses intercontinental shown that viruses isolated from Charadriiformes (gulls, terns, shorebirds) contributor outsider...
Abstract Models of host-microbe dynamics typically assume a single-host population infected by single pathogen. In reality, many hosts form multi-species aggregations and may be with an assemblage pathogens. We used meta-transcriptomic approach to characterize the viromes nine avian species in Anseriformes (ducks) Charadriiformes (shorebirds). This revealed presence 27 viral species, which 24 were novel, including double-stranded RNA viruses (Picobirnaviridae Reoviridae), single-stranded...
We evaluated the presence of coronaviruses by PCR in 918 Australian wild bird samples collected during 2016-17. Coronaviruses were detected 141 (15.3%) from species ducks, shorebirds and herons multiple sampling locations. Sequencing selected positive found mainly gammacoronaviruses, but also some deltacoronaviruses. The detection rate was improved using assays, as no single assay could detect all coronavirus samples. relatively conserved Orf1 amplicons that duck gammacoronaviruses similar...