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  1. Article ; Online: The Emergence and Evolution of SARS-CoV-2.

    Holmes, Edward C

    Annual review of virology

    2024  

    Abstract: The origin of SARS-CoV-2 has evoked heated debate and strong accusations, yet seemingly little resolution. I review the scientific evidence on the origin of SARS-CoV-2 and its subsequent spread through the human population. The available data clearly ... ...

    Abstract The origin of SARS-CoV-2 has evoked heated debate and strong accusations, yet seemingly little resolution. I review the scientific evidence on the origin of SARS-CoV-2 and its subsequent spread through the human population. The available data clearly point to a natural zoonotic emergence within, or closely linked to, the Huanan Seafood Wholesale Market in Wuhan. There is no direct evidence linking the emergence of SARS-CoV-2 to laboratory work conducted at the Wuhan Institute of Virology. The subsequent global spread of SARS-CoV-2 was characterized by a gradual adaptation to humans, with dual increases in transmissibility and virulence until the emergence of the Omicron variant. Of note has been the frequent transmission of SARS-CoV-2 from humans to other animals, marking it as a strongly host generalist virus. Unless lessons from the origin of SARS-CoV-2 are learned, it is inevitable that more zoonotic events leading to more epidemics and pandemics will plague human populations.
    Language English
    Publishing date 2024-04-17
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2764224-0
    ISSN 2327-0578 ; 2327-056X
    ISSN (online) 2327-0578
    ISSN 2327-056X
    DOI 10.1146/annurev-virology-093022-013037
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: COVID-19-lessons for zoonotic disease.

    Holmes, Edward C

    Science (New York, N.Y.)

    2022  Volume 375, Issue 6585, Page(s) 1114–1115

    Abstract: Disease emergence is driven by human-animal contact in a global viral ecosystem. ...

    Abstract Disease emergence is driven by human-animal contact in a global viral ecosystem.
    MeSH term(s) Animals ; Animals, Wild/virology ; COVID-19 ; Climate Change ; Communicable Diseases, Emerging/epidemiology ; Disease Reservoirs ; Host Adaptation ; Host-Pathogen Interactions ; Humans ; Mammals/virology ; Viral Zoonoses/epidemiology ; Viral Zoonoses/prevention & control ; Viral Zoonoses/transmission ; Viral Zoonoses/virology ; Virus Diseases/epidemiology ; Virus Diseases/prevention & control ; Virus Diseases/transmission ; Virus Diseases/virology
    Language English
    Publishing date 2022-03-10
    Publishing country United States
    Document type News
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.abn2222
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: The Ecology of Viral Emergence.

    Holmes, Edward C

    Annual review of virology

    2022  Volume 9, Issue 1, Page(s) 173–192

    Abstract: The coronavirus disease 2019 (COVID-19) pandemic has had a profound impact on human health, economic well-being, and societal function. It is essential that we use this generational experience to better understand the processes that underpin the ... ...

    Abstract The coronavirus disease 2019 (COVID-19) pandemic has had a profound impact on human health, economic well-being, and societal function. It is essential that we use this generational experience to better understand the processes that underpin the emergence of COVID-19 and other zoonotic diseases. Herein, I review the mechanisms that determine why and how viruses emerge in new hosts, as well as the barriers to this process. I show that traditional studies of virus emergence have an inherent anthropocentric bias, with disease in humans considered the inevitable outcome of virus emergence, when in reality viruses are integral components of a global ecosystem characterized by continual host jumping with humans also transmitting their viruses to other animals. I illustrate these points using coronaviruses, including severe acute respiratory syndrome coronavirus 2, as a case study. I also outline the potential steps that can be followed to help mitigate and prevent future pandemics, with combating climate change a central component.
    MeSH term(s) Animals ; COVID-19 ; Ecosystem ; Humans ; Pandemics ; SARS-CoV-2 ; Viruses ; Zoonoses/epidemiology
    Language English
    Publishing date 2022-06-15
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2764224-0
    ISSN 2327-0578 ; 2327-056X
    ISSN (online) 2327-0578
    ISSN 2327-056X
    DOI 10.1146/annurev-virology-100120-015057
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  4. Article ; Online: Through an ecological lens: An ecosystem-based approach to zoonotic risk assessment: An ecosystem-based approach to zoonotic risk assessment.

    Petrone, Mary E / Holmes, Edward C / Harvey, Erin

    EMBO reports

    2023  Volume 24, Issue 2, Page(s) e56578

    Abstract: Public health strategies to mitigate the emergence of novel pathogenic viruses should implement longitudinal metagenomic surveillance of ecosystems experiencing biodiversity changes to identify generalist viruses. ...

    Abstract Public health strategies to mitigate the emergence of novel pathogenic viruses should implement longitudinal metagenomic surveillance of ecosystems experiencing biodiversity changes to identify generalist viruses.
    MeSH term(s) Ecosystem ; Biodiversity ; Viruses ; Public Health ; Risk Assessment
    Language English
    Publishing date 2023-01-18
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2020896-0
    ISSN 1469-3178 ; 1469-221X
    ISSN (online) 1469-3178
    ISSN 1469-221X
    DOI 10.15252/embr.202256578
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  5. Article ; Online: Diversity and evolution of the animal virome.

    Harvey, Erin / Holmes, Edward C

    Nature reviews. Microbiology

    2022  Volume 20, Issue 6, Page(s) 321–334

    Abstract: The COVID-19 pandemic has given the study of virus evolution and ecology new relevance. Although viruses were first identified more than a century ago, we likely know less about their diversity than that of any other biological entity. Most documented ... ...

    Abstract The COVID-19 pandemic has given the study of virus evolution and ecology new relevance. Although viruses were first identified more than a century ago, we likely know less about their diversity than that of any other biological entity. Most documented animal viruses have been sampled from just two phyla - the Chordata and the Arthropoda - with a strong bias towards viruses that infect humans or animals of economic and social importance, often in association with strong disease phenotypes. Fortunately, the recent development of unbiased metagenomic next-generation sequencing is providing a richer view of the animal virome and shedding new light on virus evolution. In this Review, we explore our changing understanding of the diversity, composition and evolution of the animal virome. We outline the factors that determine the phylogenetic diversity and genomic structure of animal viruses on evolutionary timescales and show how this impacts assessment of the risk of disease emergence in the short term. We also describe the ongoing challenges in metagenomic analysis and outline key themes for future research. A central question is how major events in the evolutionary history of animals, such as the origin of the vertebrates and periodic mass extinction events, have shaped the diversity and evolution of the viruses they carry.
    MeSH term(s) Animals ; COVID-19 ; Genome, Viral ; Humans ; Pandemics ; Phylogeny ; Virome/genetics ; Viruses/genetics
    Language English
    Publishing date 2022-01-04
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2139054-X
    ISSN 1740-1534 ; 1740-1526
    ISSN (online) 1740-1534
    ISSN 1740-1526
    DOI 10.1038/s41579-021-00665-x
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  6. 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
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  7. 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
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  8. Article: Resolving deep evolutionary relationships within the RNA virus phylum

    Sadiq, Sabrina / Chen, Yan-Mei / Zhang, Yong-Zhen / Holmes, Edward C

    Virus evolution

    2022  Volume 8, Issue 1, Page(s) veac055

    Abstract: The RNA virus ... ...

    Abstract The RNA virus phylum
    Language English
    Publishing date 2022-06-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 2818949-8
    ISSN 2057-1577
    ISSN 2057-1577
    DOI 10.1093/ve/veac055
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  9. Article ; Online: Evolutionary stasis of viruses?

    Holmes, Edward C / Duchêne, Sebastián

    Nature reviews. Microbiology

    2019  Volume 17, Issue 5, Page(s) 329

    MeSH term(s) Adaptation, Physiological ; Biological Evolution ; Viruses
    Language English
    Publishing date 2019-03-20
    Publishing country England
    Document type Letter ; Comment
    ZDB-ID 2139054-X
    ISSN 1740-1534 ; 1740-1526
    ISSN (online) 1740-1534
    ISSN 1740-1526
    DOI 10.1038/s41579-019-0168-7
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  10. Article ; Online: Complexities of Estimating Evolutionary Rates in Viruses.

    Holmes, Edward C

    Journal of virology

    2016  Volume 90, Issue 4, Page(s) 2155

    MeSH term(s) Evolution, Molecular ; Genetic Variation ; Influenza A virus/genetics ; Models, Biological ; Selection, Genetic
    Language English
    Publishing date 2016-02
    Publishing country United States
    Document type Comment ; Letter
    ZDB-ID 80174-4
    ISSN 1098-5514 ; 0022-538X
    ISSN (online) 1098-5514
    ISSN 0022-538X
    DOI 10.1128/JVI.02570-15
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