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  1. Article ; Online: Host adaptive radiation is associated with rapid virus diversification and cross-species transmission in African cichlid fishes.

    Costa, Vincenzo A / Ronco, Fabrizia / Mifsud, Jonathon C O / Harvey, Erin / Salzburger, Walter / Holmes, Edward C

    Current biology : CB

    2024  Volume 34, Issue 6, Page(s) 1247–1257.e3

    Abstract: Adaptive radiations are generated through a complex interplay of biotic and abiotic factors. Although adaptive radiations have been widely studied in the context of animal and plant evolution, little is known about how they impact the evolution of the ... ...

    Abstract Adaptive radiations are generated through a complex interplay of biotic and abiotic factors. Although adaptive radiations have been widely studied in the context of animal and plant evolution, little is known about how they impact the evolution of the viruses that infect these hosts, which in turn may provide insights into the drivers of cross-species transmission and hence disease emergence. We examined how the rapid adaptive radiation of the cichlid fishes of African Lake Tanganyika over the last 10 million years has shaped the diversity and evolution of the viruses they carry. Through metatranscriptomic analysis of 2,242 RNA sequencing libraries, we identified 121 vertebrate-associated viruses among various tissue types that fell into 13 RNA and 4 DNA virus groups. Host-switching was commonplace, particularly within the Astroviridae, Metahepadnavirus, Nackednavirus, Picornaviridae, and Hepacivirus groups, occurring more frequently than in other fish communities. A time-calibrated phylogeny revealed that hepacivirus diversification was not constant throughout the cichlid radiation but accelerated 2-3 million years ago, coinciding with a period of rapid cichlid diversification and niche packing in Lake Tanganyika, thereby providing more closely related hosts for viral infection. These data depict a dynamic virus ecosystem within the cichlids of Lake Tanganyika, characterized by rapid virus diversification and frequent host jumping, and likely reflecting their close phylogenetic relationships that lower the barriers to cross-species virus transmission.
    MeSH term(s) Animals ; Phylogeny ; Ecosystem ; Tanzania ; Lakes ; Cichlids ; Viruses
    Language English
    Publishing date 2024-02-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 1071731-6
    ISSN 1879-0445 ; 0960-9822
    ISSN (online) 1879-0445
    ISSN 0960-9822
    DOI 10.1016/j.cub.2024.02.008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3208: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  2. Article: Divergent hepaciviruses, delta-like viruses, and a chu-like virus in Australian marsupial carnivores (dasyurids).

    Harvey, Erin / Mifsud, Jonathon C O / Holmes, Edward C / Mahar, Jackie E

    Virus evolution

    2023  Volume 9, Issue 2, Page(s) vead061

    Abstract: Although Australian marsupials are characterised by unique biology and geographic isolation, little is known about the viruses present in these iconic wildlife species. The Dasyuromorphia are an order of marsupial carnivores found only in Australia that ... ...

    Abstract Although Australian marsupials are characterised by unique biology and geographic isolation, little is known about the viruses present in these iconic wildlife species. The Dasyuromorphia are an order of marsupial carnivores found only in Australia that include both the extinct Tasmanian tiger (thylacine) and the highly threatened Tasmanian devil. Several other members of the order are similarly under threat of extinction due to habitat loss, hunting, disease, and competition and predation by introduced species such as feral cats. We utilised publicly available RNA-seq data from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database to document the viral diversity within four Dasyuromorph species. Accordingly, we identified fifteen novel virus sequences from five DNA virus families (Adenoviridae, Anelloviridae, Gammaherpesvirinae, Papillomaviridae, and Polyomaviridae) and three RNA virus taxa: the order Jingchuvirales, the genus
    Language English
    Publishing date 2023-10-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 2818949-8
    ISSN 2057-1577
    ISSN 2057-1577
    DOI 10.1093/ve/vead061
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Australian terrestrial environments harbour extensive RNA virus diversity.

    Sadiq, Sabrina / Harvey, Erin / Mifsud, Jonathon C O / Minasny, Budiman / McBratney, Alex B / Pozza, Liana E / Mahar, Jackie E / Holmes, Edward C

    Virology

    2024  Volume 593, Page(s) 110007

    Abstract: Australia is home to a diverse range of unique native fauna and flora. To address whether Australian ecosystems also harbour unique viruses, we performed meta-transcriptomic sequencing of 16 farmland and sediment samples taken from the east and west ... ...

    Abstract Australia is home to a diverse range of unique native fauna and flora. To address whether Australian ecosystems also harbour unique viruses, we performed meta-transcriptomic sequencing of 16 farmland and sediment samples taken from the east and west coasts of Australia. We identified 2460 putatively novel RNA viruses across 18 orders, the vast majority of which belonged to the microbe-associated phylum Lenarviricota. In many orders, such as the Nodamuvirales and Ghabrivirales, the novel viruses identified here comprised entirely new clades. Novel viruses also fell between established genera or families, such as in the Cystoviridae and Picornavirales, while highly divergent lineages were identified in the Sobelivirales and Ghabrivirales. Viral read abundance and alpha diversity were influenced by sampling site, soil type and land use, but not by depth from the surface. In sum, Australian soils and sediments are home to remarkable viral diversity, reflecting the biodiversity of local fauna and flora.
    MeSH term(s) Humans ; Ecosystem ; Australia ; Phylogeny ; RNA Viruses/genetics ; Viruses
    Language English
    Publishing date 2024-02-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 200425-2
    ISSN 1096-0341 ; 0042-6822
    ISSN (online) 1096-0341
    ISSN 0042-6822
    DOI 10.1016/j.virol.2024.110007
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Ud II Zs.172: Show issues Location:
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  4. Article ; Online: Transcriptome Mining Expands Knowledge of RNA Viruses across the Plant Kingdom.

    Mifsud, Jonathon C O / Gallagher, Rachael V / Holmes, Edward C / Geoghegan, Jemma L

    Journal of virology

    2022  , Page(s) e0026022

    Abstract: Our current understanding of plant viruses stems largely from those affecting economically important plants. Yet plant species in cultivation represent a small and biased subset of the plant kingdom. Here, we describe virus diversity and abundance in 1, ... ...

    Abstract Our current understanding of plant viruses stems largely from those affecting economically important plants. Yet plant species in cultivation represent a small and biased subset of the plant kingdom. Here, we describe virus diversity and abundance in 1,079 transcriptomes from species across the breadth of the plant kingdom (Archaeplastida) by analyzing open-source data from the 1000 Plant Transcriptomes Initiative (1KP). We identified 104 potentially novel viruses, of which 40% were single-stranded positive-sense RNA viruses across eight orders, including members of the
    Language English
    Publishing date 2022-05-31
    Publishing country United States
    Document type Journal Article
    ZDB-ID 80174-4
    ISSN 1098-5514 ; 0022-538X
    ISSN (online) 1098-5514
    ISSN 0022-538X
    DOI 10.1128/jvi.00260-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 609: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  5. Article: Limited cross-species virus transmission in a spatially restricted coral reef fish community.

    Costa, Vincenzo A / Bellwood, David R / Mifsud, Jonathon C O / Van Brussel, Kate / Geoghegan, Jemma L / Holmes, Edward C / Harvey, Erin

    Virus evolution

    2023  Volume 9, Issue 1, Page(s) vead011

    Abstract: The Great Barrier Reef (GBR)-the largest coral reef ecosystem in the world-supports over 1,200 fish species with some of the highest population densities and diversities observed in vertebrates, offering a high potential for virus transmission among ... ...

    Abstract The Great Barrier Reef (GBR)-the largest coral reef ecosystem in the world-supports over 1,200 fish species with some of the highest population densities and diversities observed in vertebrates, offering a high potential for virus transmission among species. As such, the GBR represents an exceptional natural ecosystem to determine the impact of host community diversity on virus evolution and emergence. In recent decades, the GBR has also experienced significant threats of extinction, making it one of the most vulnerable ecosystems on the planet. Despite the global importance of the GBR, our understanding of virus diversity and connectivity in tropical reef fishes remains poor. Here, we employed metatranscriptomic sequencing to reveal the viromes of sixty-one reef fish species. This identified transcripts representing 132 putative viral sequences, 38 of which exhibited strong phylogenetic relationships with known vertebrate-associated viral genera, including a novel
    Language English
    Publishing date 2023-02-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 2818949-8
    ISSN 2057-1577
    ISSN 2057-1577
    DOI 10.1093/ve/vead011
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Evidence for an ancient aquatic origin of the RNA viral order

    Petrone, Mary E / Parry, Rhys / Mifsud, Jonathon C O / Van Brussel, Kate / Vorhees, Ian E H / Richards, Zoe T / Holmes, Edward C

    Proceedings of the National Academy of Sciences of the United States of America

    2023  Volume 120, Issue 45, Page(s) e2310529120

    Abstract: The emergence of previously unknown disease-causing viruses in mammals is in part the result of a long-term evolutionary process. Reconstructing the deep phylogenetic histories of viruses helps identify major evolutionary transitions and contextualizes ... ...

    Abstract The emergence of previously unknown disease-causing viruses in mammals is in part the result of a long-term evolutionary process. Reconstructing the deep phylogenetic histories of viruses helps identify major evolutionary transitions and contextualizes the emergence of viruses in new hosts. We used a combination of total RNA sequencing and transcriptome data mining to extend the diversity and evolutionary history of the RNA virus order
    MeSH term(s) Animals ; Humans ; Phylogeny ; RNA Viruses/genetics ; Influenza, Human ; Invertebrates/genetics ; Orthomyxoviridae/genetics ; RNA ; Evolution, Molecular ; RNA, Viral/genetics ; Mammals/genetics
    Chemical Substances RNA (63231-63-0) ; RNA, Viral
    Language English
    Publishing date 2023-10-31
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2310529120
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1148: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  7. Article: Transcriptome mining extends the host range of the

    Mifsud, Jonathon C O / Costa, Vincenzo A / Petrone, Mary E / Marzinelli, Ezequiel M / Holmes, Edward C / Harvey, Erin

    Virus evolution

    2022  Volume 9, Issue 1, Page(s) veac124

    Abstract: The flavivirids ( ... ...

    Abstract The flavivirids (family
    Language English
    Publishing date 2022-12-26
    Publishing country England
    Document type Journal Article
    ZDB-ID 2818949-8
    ISSN 2057-1577
    ISSN 2057-1577
    DOI 10.1093/ve/veac124
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Metagenomic sequencing reveals a lack of virus exchange between native and invasive freshwater fish across the Murray-Darling Basin, Australia.

    Costa, Vincenzo A / Mifsud, Jonathon C O / Gilligan, Dean / Williamson, Jane E / Holmes, Edward C / Geoghegan, Jemma L

    Virus evolution

    2021  Volume 7, Issue 1, Page(s) veab034

    Abstract: Biological invasions are among the biggest threats to freshwater biodiversity. This is increasingly relevant in the Murray-Darling Basin, Australia, particularly since the introduction of the common carp ( ...

    Abstract Biological invasions are among the biggest threats to freshwater biodiversity. This is increasingly relevant in the Murray-Darling Basin, Australia, particularly since the introduction of the common carp (
    Language English
    Publishing date 2021-04-13
    Publishing country England
    Document type Journal Article
    ZDB-ID 2818949-8
    ISSN 2057-1577
    ISSN 2057-1577
    DOI 10.1093/ve/veab034
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the

    Miller, Allison K / Mifsud, Jonathon C O / Costa, Vincenzo A / Grimwood, Rebecca M / Kitson, Jane / Baker, Cindy / Brosnahan, Cara L / Pande, Anjali / Holmes, Edward C / Gemmell, Neil J / Geoghegan, Jemma L

    Virus evolution

    2021  Volume 7, Issue 2, Page(s) veab050

    Abstract: ... ...

    Abstract The
    Language English
    Publishing date 2021-05-31
    Publishing country England
    Document type Journal Article
    ZDB-ID 2818949-8
    ISSN 2057-1577
    ISSN 2057-1577
    DOI 10.1093/ve/veab050
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Virome composition in marine fish revealed by meta-transcriptomics.

    Geoghegan, Jemma L / Di Giallonardo, Francesca / Wille, Michelle / Ortiz-Baez, Ayda Susana / Costa, Vincenzo A / Ghaly, Timothy / Mifsud, Jonathon C O / Turnbull, Olivia M H / Bellwood, David R / Williamson, Jane E / Holmes, Edward C

    Virus evolution

    2021  Volume 7, Issue 1, Page(s) veab005

    Abstract: Revealing the determinants of virome composition is central to placing disease emergence in a broader evolutionary context. Fish are the most species-rich group of vertebrates and so provide an ideal model system to study the factors that shape virome ... ...

    Abstract Revealing the determinants of virome composition is central to placing disease emergence in a broader evolutionary context. Fish are the most species-rich group of vertebrates and so provide an ideal model system to study the factors that shape virome compositions and their evolution. We characterized the viromes of nineteen wild-caught species of marine fish using total RNA sequencing (meta-transcriptomics) combined with analyses of sequence and protein structural homology to identify divergent viruses that often evade characterization. From this, we identified twenty-five new vertebrate-associated viruses and a further twenty-two viruses likely associated with fish diet or their microbiomes. The vertebrate-associated viruses identified here included the first fish virus in the
    Language English
    Publishing date 2021-02-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 2818949-8
    ISSN 2057-1577
    ISSN 2057-1577
    DOI 10.1093/ve/veab005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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