Biology subjects

Eden, J.-S.

Publications and source records attributed to Eden, J.-S..

25 records · Page 2Linked to original sources

bioRxiv2019

Matryoshka RNA virus 1: a novel RNA virus associated with Plasmodium parasites in human malaria

Parasites of the genus Plasmodium cause human malaria. Yet nothing is known about the viruses that infect these divergent eukaryotes. We investigated the Plasmodium virome by performing a meta-transcriptomic analysis of blood samples from malaria patients infected with P. vivax, P. falciparum or P. knowlesi. This revealed a novel bi-segmented narna-like RNA virus restricted to P. vivax and named Matryoshka RNA virus 1 (MaRNAV-1) to reflect its \"Russian doll\" nature: a virus, infecting a parasite, infecting an animal. MaRNAV-1 was abundant in geographically diverse P. vivax from humans and mosquitoes. Notably, a related virus (MaRNAV-2) was identified in Australian birds infected with a Leucocytozoon - eukaryotic parasites that group with Plasmodium in the Apicomplexa subclass hematozoa. This is the first report of a Plasmodium virus. As well as broadening our understanding of the eukaryotic virosphere, the restriction to P. vivax may help understand P. vivax-specific biology in humans and mosquitoes.

evolutionary biology↗

bioRxiv2019

Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities

High-throughput sequencing (HTS) enables the generation of large amounts of genome sequence data at a reasonable cost. Organisms in mixed microbial communities can now be sequenced and identified in a culture-independent way, usually using amplicon sequencing of a DNA barcode. Bulk RNA-seq (metatranscriptomics) has several advantages over DNA-based amplicon sequencing: it is less susceptible to amplification biases, it captures only living organisms, and it enables a larger set of genes to be used for taxonomic identification. Using a defined mock community comprised of 17 fungal isolates, we evaluated whether metatranscriptomics can accurately identify fungal species and subspecies in mixed communities. Overall, 72.9% of the RNA transcripts were classified, from which the vast majority (99.5%) were correctly identified at the species-level. Of the 15 species sequenced, 13 were retrieved and identified correctly. We also detected strain-level variation within the Cryptococcus species complexes: 99.3% of transcripts assigned to Cryptococcus were classified as one of the four strains used in the mock community. Laboratory contaminants and/or misclassifications were diverse but represented only 0.44% of the transcripts. Hence, these results show that it is possible to obtain accurate species- and strain-level fungal identification from metatranscriptome data as long as taxa identified at low abundance are discarded to avoid false-positives derived from contamination or misclassifications. This study therefore establishes a base-line for the application of metatranscriptomics in clinical mycology and ecological studies.

molecular biology↗

bioRxiv2019

Novel hepatitis D-like agents in vertebrates and invertebrates

Hepatitis delta virus (HDV) is the smallest known RNA virus and encodes a single protein. Until recently, HDV had only been identified in humans, where it is strongly associated with co-infection with hepatitis B virus (HBV). However, the recent discovery of HDV-like viruses in metagenomic samples from birds and snakes suggests that this virus has a far longer evolutionary history. Herein, using additional meta-transcriptomic data, we show that highly divergent HDV-like viruses are also present in fish, amphibians and invertebrates. Notably, the novel viruses identified here share HDV-like genomic features such as a small genome size of ~1.7kb in length, circular genomes, and self-complementary, unbranched rod-like structures. Coiled-coil domains, leucine zippers, conserved residues with essential biological functions and isoelectronic points similar to those in the human hepatitis delta virus antigens (HDAgs) were also identified in the putative non-human HDAgs. Notably, none of these novel HDV-like viruses were associated with hepadnavirus infection, supporting the idea that the HDV-HBV association may be specific to humans. Collectively, these data not only broaden our understanding of the diversity and host range of HDV in non-human species, but shed light on its origin and evolutionary history.

evolutionary biology↗

bioRxiv2018

Punctuated evolution of myxoma virus: rapid and disjunct evolution of a recent viral lineage in Australia

Myxoma virus (MYXV) has been evolving in a novel host species - European rabbits - in Australia since 1950. Previous studies of viruses sampled from 1950 to 1999 revealed a remarkably clock-like evolutionary process across all Australian lineages of MYXV. Through an analysis of 49 newly generated MYXV genome sequences isolated in Australia between 2008 and 2017 we show that MYXV evolution in Australia can be characterized by three lineages, one of which exhibited a greatly elevated rate of evolutionary change and a dramatic break-down of temporal structure. Phylogenetic analysis revealed that this apparently punctuated evolutionary event occurred between 1996 and 2012. The branch leading to the rapidly evolving lineage contained a relatively high number of non-synonymous substitutions, and viruses in this lineage reversed a mutation found in the progenitor standard laboratory strain (SLS) and all previous sequences that disrupts the reading frame of the M005L/R gene. Analysis of genes encoding proteins involved in DNA synthesis or RNA transcription did not reveal any mutations likely to cause rapid evolution. Although there was some evidence for recombination across the MYXV phylogeny, this was not associated with the increase in evolutionary rate. The period from 1996 to 2012 saw significant declines in wild rabbit numbers, due to the introduction of rabbit hemorrhagic disease and prolonged drought in south-eastern Australia, followed by the partial recovery of populations. We therefore suggest that a rapidly changing environment for virus transmission changed the selection pressures faced by MYXV and altered the course of virus evolution.\n\nIMPORTANCEThe co-evolution of myxoma virus (MYXV) and European rabbits in Australia is one of the most important natural experiments in evolutionary biology, providing insights into virus adaptation to new hosts and the evolution of virulence. Previous studies of MYXV evolution have also shown that the virus evolves both relatively rapidly and in a strongly clock-like manner. Using newly acquired MYXV genome sequences from Australia we show that the virus has experienced a dramatic change in evolutionary behavior over the last 20 years, with a break-down in clock-like structure, the appearance of a rapidly evolving virus lineage, and the accumulation of multiple non-synonymous and indel mutations. We suggest that this punctuated evolutionary event likely reflects a change in selection pressures as rabbit numbers declined following the introduction of rabbit hemorrhagic disease virus and drought in the geographic regions inhabited by rabbits.

evolutionary biology↗

bioRxiv2018

High levels of antibiotic resistance gene expression among birds living in a wastewater treatment plant

Antibiotic resistance is rendering common bacterial infections untreatable. Wildlife can incorporate and disperse antibiotic resistant bacteria in the environment, such as water systems, which in turn serve as reservoirs of resistance genes for human pathogens. We used bulk RNA-sequencing (meta-transcriptomics) to assess the diversity and expression levels of functionally active resistance genes in the microbiome of birds with aquatic behavior. We sampled birds across a range of habitats, from penguins in Antarctica to ducks in a wastewater treatment plant in Australia. This revealed 81 antibiotic resistance genes in birds from all localities, including {beta}-lactam, tetracycline and chloramphenicol resistance in Antarctica, and genes typically associated with multidrug resistance plasmids in areas with high human impact. Notably, birds feeding at a wastewater treatment plant carried the greatest resistance gene burden, suggesting that human waste, even if it undergoes treatment, contributes to the spread of antibiotic resistance genes to the wild. Differences in resistance gene burden also reflected the birds ecology, taxonomic group and microbial functioning. Ducks, which feed by dabbling, carried a higher abundance and diversity of resistance genes than turnstones, avocets and penguins, that usually prey on more pristine waters. In sum, this study helps to reveal the complex factors explaining the distribution of resistance genes and their exchange routes between humans and wildlife.

ecology↗

bioRxiv2018

A divergent hepatitis D-like agent in birds

Hepatitis delta virus (HDV) is currently only found in humans, and is a satellite virus that depends on hepatitis B virus (HBV) envelope proteins for assembly, release and entry. Using meta-transcriptomics, we identified the genome of a novel HDV-like agent in ducks. Sequence analysis revealed secondary structures that were shared with HDV, including self-complementarity and ribozyme features. The predicted viral protein shares 32% amino acid similarity to the small delta antigen of HDV and comprises a divergent phylogenetic lineage. The discovery of an avian HDV-like agent has important implications for the understanding of the origins of HDV and subviral agents.\n\nImportanceHepatitis delta virus (HDV) is currently only found in humans, and coinfections of HDV and Hepatitis B virus (HBV) in humans result in severe liver disease. There are a number of hypotheses for the origin of HDV, although a key component of all is that HDV only exists in humans. Here, we describe a novel deltavirus-like agent identified in wild birds. Although this agent is genetically divergent, it exhibits important similarities to HDV, such as the presence of ribosymes and self-complementarity. The discovery of an avian HDV-like agent challenges our understanding of both the origin and the co-evolutionary relationships of subviral agents with helper viruses.

molecular biology↗

bioRxiv2018

Extensive Diversity of RNA Viruses in Australian Ticks

Understanding the microbiome of ticks in Australia is of considerable interest given the ongoing debate over whether Lyme disease, and its causative agent the bacterium Borrelia burgdorferi senso lato, are present in Australia. The diversity of bacteria infecting Australian ticks has been the subject of a number of studies using both culture and metagenomics based techniques. However, little is known about the virome of Australian ticks, including those that may have the potential to infect mammalian species. We used a meta-transcriptomics approach to reveal the viral diversity within Australian ticks collected from two locations on the central-east coast of Australia, including metropolitan Sydney. From this we identified 19 novel species of RNA virus belonging to 10 families, as well as one previously described RNA virus. The majority of these viruses clustered phylogenetically with arthropod-associated viruses suggesting that they do not utilize mammalian hosts. However, two novel viruses discovered in ticks feeding on bandicoot marsupials clustered closely within the mammalian associated Hepacivirus and Pestivirus genera (Flaviviridae). Notably, another bandicoot tick yielded a novel Coltivirus (Reoviridae) - a group of largely tick-associated viruses containing the known human pathogen Colorado tick fever virus and its relative Eyach virus. Importantly, our transcriptomic data provided no evidence for the presence of B. burgdorferi s.l.. in any tick sample, providing further evidence against the presence of Lyme Disease in Australia. In sum, this study reveals that Australian ticks harbor a diverse virome, including some viruses that merit additional screening in the context of emerging infectious disease.\n\nIMPORTANCEEach year a growing number of individuals along the east coast of Australia experience debilitating disease following tick bites. As there is no evidence for the presence of the causative agent of Lyme disease, Borrelia Burgdorferi seno lato, in Australian ticks, the etiological basis of this disease syndrome remains controversial. To characterize the viruses associated with Australian ticks, particularly those that might be associated with mammalian infection, we performed unbiased RNA sequencing on 146 ticks collected across two locations along the coast of New South Wales, Australia. This revealed 19 novel RNA viruses from a diverse set of families. Notably, three of these viruses were related to known mammalian viruses, including one that fell within the genus Coltivirus and related to the human pathogen, Colorado tick fever virus.

microbiology↗