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  1. Article ; Online: How accurately can we assess zoonotic risk?

    Michelle Wille / Jemma L Geoghegan / Edward C Holmes

    PLoS Biology, Vol 19, Iss 4, p e

    2021  Volume 3001135

    Abstract: Identifying the animal reservoirs from which zoonotic viruses will likely emerge is central to understanding the determinants of disease emergence. Accordingly, there has been an increase in studies attempting zoonotic "risk assessment." Herein, we ... ...

    Abstract Identifying the animal reservoirs from which zoonotic viruses will likely emerge is central to understanding the determinants of disease emergence. Accordingly, there has been an increase in studies attempting zoonotic "risk assessment." Herein, we demonstrate that the virological data on which these analyses are conducted are incomplete, biased, and rapidly changing with ongoing virus discovery. Together, these shortcomings suggest that attempts to assess zoonotic risk using available virological data are likely to be inaccurate and largely only identify those host taxa that have been studied most extensively. We suggest that virus surveillance at the human-animal interface may be more productive.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2021-04-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Meta-transcriptomic analysis of the virome and microbiome of the invasive Indian myna (Acridotheres tristis) in Australia

    Wei-Shan Chang / Karrie Rose / Edward C. Holmes

    One Health, Vol 13, Iss , Pp 100360- (2021)

    2021  

    Abstract: Invasive species exert a serious impact on native fauna and flora and have become the target of eradication and management efforts worldwide. Invasive avian species can also be important pathogen reservoirs, although their viromes and microbiomes have ... ...

    Abstract Invasive species exert a serious impact on native fauna and flora and have become the target of eradication and management efforts worldwide. Invasive avian species can also be important pathogen reservoirs, although their viromes and microbiomes have rarely been studied. As one of the top 100 invasive pest species globally, the expansion of Indian mynas (Acridotheres tristis) into peri-urban and rural environments, in conjunction with increasing free-ranging avian agricultural practices, may increase the risk of microbial pathogens jumping species boundaries. Herein, we used a meta-transcriptomic approach to explore the microbes present in brain, liver and large intestine of 16 invasive Indian myna birds in Sydney, Australia. From this, we discovered seven novel viruses from the families Adenoviridae, Caliciviridae, Flaviviridae, Parvoviridae and Picornaviridae. Interestingly, each of the novel viruses identified shared less than 80% genomic similarity with their closest relatives from other avian species, indicative of a lack of detectable virus transmission between invasive mynas to native or domestic species. Of note, we also identified two coccidian protozoa, Isospora superbusi and Isospora greineri, from the liver and gut tissues of mynas. Overall, these data demonstrate that invasive mynas can harbor a diversity of viruses and other microorganisms such that ongoing pathogen surveillance in this species is warranted.
    Keywords Meta-transcriptomics ; myna ; Pegivirus ; Calicivirus ; Chaphamaparvovirus ; Isospora ; Medicine (General) ; R5-920
    Subject code 590
    Language English
    Publishing date 2021-12-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Pandemics–Keep Calm and Carry On.

    Edward C. Holmes

    PLoS Biology, Vol 12, Iss

    2014  Volume 2

    Abstract: Evolutionary biologist Edward Holmes reviews Peter Doherty's ... ...

    Abstract Evolutionary biologist Edward Holmes reviews Peter Doherty's book
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2014-02-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Response to Brinkmann et al. “Re-assembly of 19th century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the United States”

    Ana T. Duggan / Edward C. Holmes / Hendrik N. Poinar

    Genome Biology, Vol 21, Iss 1, Pp 1-

    2020  Volume 2

    Abstract: Abstract We thank Brinkmann and colleagues for their correspondence and their further investigation into these American Civil War Era vaccination strains. Here, we summarize the difficulties and caveats of work with ancient DNA. ...

    Abstract Abstract We thank Brinkmann and colleagues for their correspondence and their further investigation into these American Civil War Era vaccination strains. Here, we summarize the difficulties and caveats of work with ancient DNA.
    Keywords Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
    Language English
    Publishing date 2020-12-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: The Biological Object Notation (BON)

    Jan P. Buchmann / Mathieu Fourment / Edward C. Holmes

    Scientific Reports, Vol 8, Iss 1, Pp 1-

    a structured file format for biological data

    2018  Volume 8

    Abstract: Abstract The large size and high complexity of biological data can represent a major methodological challenge for the analysis and exchange of data sets between computers and applications. There has also been a substantial increase in the amount of ... ...

    Abstract Abstract The large size and high complexity of biological data can represent a major methodological challenge for the analysis and exchange of data sets between computers and applications. There has also been a substantial increase in the amount of metadata associated with biological data sets, which is being increasingly incorporated into existing data formats. Despite the existence of structured formats based on XML, biological data sets are mainly formatted using unstructured file formats, and the incorporation of metadata results in increasingly complex parsing routines such that they become more error prone. To overcome these problems, we present the “biological object notation” (BON) format, a new way to exchange and parse nearly all biological data sets more efficiently and with less error than other currently available formats. Based on JavaScript Object Notation (JSON), BON simplifies parsing by clearly separating the biological data from its metadata and reduces complexity compared to XML based formats. The ability to selectively compress data up to 87% compared to other file formats and the reduced complexity results in improved transfer times and less error prone applications.
    Keywords Medicine ; R ; Science ; Q
    Subject code 004 ; 612
    Language English
    Publishing date 2018-06-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Unmapped RNA Virus Diversity in Termites and their Symbionts

    Callum Le Lay / Mang Shi / Aleš Buček / Thomas Bourguignon / Nathan Lo / Edward C. Holmes

    Viruses, Vol 12, Iss 1145, p

    2020  Volume 1145

    Abstract: Despite their ecological importance, nothing is known about the diversity and abundance of RNA viruses in termites (Termitoidae). We used a metatranscriptomics approach to determine the RNA virome structure of 50 diverse species of termite that differ in ...

    Abstract Despite their ecological importance, nothing is known about the diversity and abundance of RNA viruses in termites (Termitoidae). We used a metatranscriptomics approach to determine the RNA virome structure of 50 diverse species of termite that differ in both phylogenetic position and colony composition. From these samples, we identified 67 novel RNA viruses, characterized their genomes, quantified their abundance and inferred their evolutionary history. These viruses were found within or similar to those from the Togaviridae, Iflaviridae, Polycipiviridae, Flaviviridae, Leviviridae, Narnaviridae, Mitoviridae, Lispivirdae, Phasmaviridae , Picobirnaviridae and Partitiviridae . However, all viruses identified were novel and divergent, exhibiting only 20% to 45% amino acid identity to previously identified viruses. Our analysis suggested that 17 of the viruses identified were termite-infecting, with the remainder likely associated with the termite microbiome or diet. Unclassified sobemo-like and bunya-like viruses dominated termite viromes, while most of the phylogenetic diversity was provided by the picobirna- and mitovirus-like viruses. Of note was the identification of a novel flavi-like virus most closely related to those found in marine vertebrates and invertebrates. Notably, the sampling procedure had the strongest association with virome composition, with greater RNA virome diversity in libraries prepared from whole termite bodies than those that only sampled heads.
    Keywords RNA viruses ; evolution ; ecology ; metatranscriptomics ; RNA sequencing ; termites ; Microbiology ; QR1-502
    Subject code 500
    Language English
    Publishing date 2020-10-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Predicting virus emergence amid evolutionary noise

    Jemma L. Geoghegan / Edward C. Holmes

    Open Biology, Vol 7, Iss

    2017  Volume 10

    Abstract: The study of virus disease emergence, whether it can be predicted and how it might be prevented, has become a major research topic in biomedicine. Here we show that efforts to predict disease emergence commonly conflate fundamentally different ... ...

    Abstract The study of virus disease emergence, whether it can be predicted and how it might be prevented, has become a major research topic in biomedicine. Here we show that efforts to predict disease emergence commonly conflate fundamentally different evolutionary and epidemiological time scales, and are likely to fail because of the enormous number of unsampled viruses that could conceivably emerge in humans. Although we know much about the patterns and processes of virus evolution on evolutionary time scales as depicted in family-scale phylogenetic trees, these data have little predictive power to reveal the short-term microevolutionary processes that underpin cross-species transmission and emergence. Truly understanding disease emergence therefore requires a new mechanistic and integrated view of the factors that allow or prevent viruses spreading in novel hosts. We present such a view, suggesting that both ecological and genetic aspects of virus emergence can be placed within a simple population genetic framework, which in turn highlights the importance of host population size and density in determining whether emergence will be successful. Despite this framework, we conclude that a more practical solution to preventing and containing the successful emergence of new diseases entails ongoing virological surveillance at the human–animal interface and regions of ecological disturbance.
    Keywords emergence ; evolution ; phylogeny ; virus ; spill-over ; virosphere ; Biology (General) ; QH301-705.5
    Subject code 501
    Language English
    Publishing date 2017-01-01T00:00:00Z
    Publisher The Royal Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families.

    Jemma L Geoghegan / Sebastián Duchêne / Edward C Holmes

    PLoS Pathogens, Vol 13, Iss 2, p e

    2017  Volume 1006215

    Abstract: The cross-species transmission of viruses from one host species to another is responsible for the majority of emerging infections. However, it is unclear whether some virus families have a greater propensity to jump host species than others. If related ... ...

    Abstract The cross-species transmission of viruses from one host species to another is responsible for the majority of emerging infections. However, it is unclear whether some virus families have a greater propensity to jump host species than others. If related viruses have an evolutionary history of co-divergence with their hosts there should be evidence of topological similarities between the virus and host phylogenetic trees, whereas host jumping generates incongruent tree topologies. By analyzing co-phylogenetic processes in 19 virus families and their eukaryotic hosts we provide a quantitative and comparative estimate of the relative frequency of virus-host co-divergence versus cross-species transmission among virus families. Notably, our analysis reveals that cross-species transmission is a near universal feature of the viruses analyzed here, with virus-host co-divergence occurring less frequently and always on a subset of viruses. Despite the overall high topological incongruence among virus and host phylogenies, the Hepadnaviridae, Polyomaviridae, Poxviridae, Papillomaviridae and Adenoviridae, all of which possess double-stranded DNA genomes, exhibited more frequent co-divergence than the other virus families studied here. At the other extreme, the virus and host trees for all the RNA viruses studied here, particularly the Rhabdoviridae and the Picornaviridae, displayed high levels of topological incongruence, indicative of frequent host switching. Overall, we show that cross-species transmission plays a major role in virus evolution, with all the virus families studied here having the potential to jump host species, and that increased sampling will likely reveal more instances of host jumping.
    Keywords Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
    Subject code 590
    Language English
    Publishing date 2017-02-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Expanding the range of the respiratory infectome in Australian feedlot cattle with and without respiratory disease using metatranscriptomics

    Barbara P. Brito / Melinda J. Frost / Kay Anantanawat / Frederick Jaya / Tony Batterham / Steven P. Djordjevic / Wei-Shan Chang / Edward C. Holmes / Aaron E. Darling / Peter D. Kirkland

    Microbiome, Vol 11, Iss 1, Pp 1-

    2023  Volume 17

    Abstract: Abstract Background Bovine respiratory disease (BRD) is one of the most common diseases in intensively managed cattle, often resulting in high morbidity and mortality. Although several pathogens have been isolated and extensively studied, the complete ... ...

    Abstract Abstract Background Bovine respiratory disease (BRD) is one of the most common diseases in intensively managed cattle, often resulting in high morbidity and mortality. Although several pathogens have been isolated and extensively studied, the complete infectome of the respiratory complex consists of a more extensive range unrecognised species. Here, we used total RNA sequencing (i.e., metatranscriptomics) of nasal and nasopharyngeal swabs collected from animals with and without BRD from two cattle feedlots in Australia. Results A high abundance of bovine nidovirus, influenza D, bovine rhinitis A and bovine coronavirus was found in the samples. Additionally, we obtained the complete or near-complete genome of bovine rhinitis B, enterovirus E1, bovine viral diarrhea virus (sub-genotypes 1a and 1c) and bovine respiratory syncytial virus, and partial sequences of other viruses. A new species of paramyxovirus was also identified. Overall, the most abundant RNA virus, was the bovine nidovirus. Characterisation of bacterial species from the transcriptome revealed a high abundance and diversity of Mollicutes in BRD cases and unaffected control animals. Of the non-Mollicutes species, Histophilus somni was detected, whereas there was a low abundance of Mannheimia haemolytica. Conclusion This study highlights the use of untargeted sequencing approaches to study the unrecognised range of microorganisms present in healthy or diseased animals and the need to study previously uncultured viral species that may have an important role in cattle respiratory disease. Video Abstract
    Keywords Bovine respiratory disease ; Metatranscriptomics ; Metagenomics ; Infectome ; Virome ; Microbiome ; Microbial ecology ; QR100-130
    Subject code 630
    Language English
    Publishing date 2023-07-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Viromes of Freshwater Fish with Lacustrine and Diadromous Life Histories Differ in Composition

    Benjamin J. Perry / Mitra Mohamadi Darestani / Motia Gulshan Ara / Amélie Hoste / Jennifer M. Jandt / Ludovic Dutoit / Edward C. Holmes / Travis Ingram / Jemma L. Geoghegan

    Viruses, Vol 14, Iss 257, p

    2022  Volume 257

    Abstract: Viruses that infect fish are understudied, yet they provide important evolutionary context to the viruses that infect terrestrial vertebrates. We surveyed gill tissue meta-transcriptomes collected from two species of native freshwater fish from Aotearoa ... ...

    Abstract Viruses that infect fish are understudied, yet they provide important evolutionary context to the viruses that infect terrestrial vertebrates. We surveyed gill tissue meta-transcriptomes collected from two species of native freshwater fish from Aotearoa New Zealand— Retropinna retropinna and Gobiomorphus cotidianus . A total of 64 fish were used for gill tissue meta-transcriptomic sequencing, from populations with contrasting life histories—landlocked (i.e., lacustrine) and diadromous—on the South Island and Chatham Islands. We observed that both viral richness and taxonomic diversity were significantly associated with life history and host species, with lacustrine R. retropinna characterised by higher viral alpha diversity than diadromous R. retropinna . Additionally, we observed transcripts of fish viruses from 12 vertebrate host-associated virus families, and phylogenetically placed eight novel RNA viruses and three novel DNA viruses in the Astroviridae , Paramyxoviridae , Orthomyxoviridae , Rhabdoviridae , Totiviridae , Poxviridae , Alloherpesviridae, and Adintoviridae in their evolutionary contexts. These results represent an important survey of the viruses that infect two widespread native fish species in New Zealand, and provide insight useful for future fish virus surveys.
    Keywords virus ; fish ; diadromous ; lacustrine ; ecology ; meta-transcriptomics ; Microbiology ; QR1-502
    Subject code 590
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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