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  1. Article ; Online: The evolutionary drivers and correlates of viral host jumps.

    Tan, Cedric C S / van Dorp, Lucy / Balloux, Francois

    Nature ecology & evolution

    2024  

    Abstract: Most emerging and re-emerging infectious diseases stem from viruses that naturally circulate in non-human vertebrates. When these viruses cross over into humans, they can cause disease outbreaks, epidemics and pandemics. While zoonotic host jumps have ... ...

    Abstract Most emerging and re-emerging infectious diseases stem from viruses that naturally circulate in non-human vertebrates. When these viruses cross over into humans, they can cause disease outbreaks, epidemics and pandemics. While zoonotic host jumps have been extensively studied from an ecological perspective, little attention has gone into characterizing the evolutionary drivers and correlates underlying these events. To address this gap, we harnessed the entirety of publicly available viral genomic data, employing a comprehensive suite of network and phylogenetic analyses to investigate the evolutionary mechanisms underpinning recent viral host jumps. Surprisingly, we find that humans are as much a source as a sink for viral spillover events, insofar as we infer more viral host jumps from humans to other animals than from animals to humans. Moreover, we demonstrate heightened evolution in viral lineages that involve putative host jumps. We further observe that the extent of adaptation associated with a host jump is lower for viruses with broader host ranges. Finally, we show that the genomic targets of natural selection associated with host jumps vary across different viral families, with either structural or auxiliary genes being the prime targets of selection. Collectively, our results illuminate some of the evolutionary drivers underlying viral host jumps that may contribute to mitigating viral threats across species boundaries.
    Language English
    Publishing date 2024-03-25
    Publishing country England
    Document type Journal Article
    ISSN 2397-334X
    ISSN (online) 2397-334X
    DOI 10.1038/s41559-024-02353-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Coordinated surveillance is essential to monitor and mitigate the evolutionary impacts of SARS-CoV-2 spillover and circulation in animal hosts.

    Kuchipudi, Suresh V / Tan, Cedric / van Dorp, Lucy / Lichtveld, Maureen / Pickering, Bradley / Bowman, Jeff / Mubareka, Samira / Balloux, Francois

    Nature ecology & evolution

    2023  Volume 7, Issue 7, Page(s) 956–959

    MeSH term(s) Animals ; SARS-CoV-2 ; COVID-19
    Language English
    Publishing date 2023-05-25
    Publishing country England
    Document type Journal Article
    ISSN 2397-334X
    ISSN (online) 2397-334X
    DOI 10.1038/s41559-023-02082-0
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  3. Article ; Online: Author Correction: Coordinated surveillance is essential to monitor and mitigate the evolutionary impacts of SARS-CoV-2 spillover and circulation in animal hosts.

    Kuchipudi, Suresh V / Tan, Cedric / van Dorp, Lucy / Lichtveld, Maureen / Pickering, Bradley / Bowman, Jeff / Mubareka, Samira / Balloux, Francois

    Nature ecology & evolution

    2023  Volume 7, Issue 7, Page(s) 1152

    Language English
    Publishing date 2023-06-19
    Publishing country England
    Document type Published Erratum
    ISSN 2397-334X
    ISSN (online) 2397-334X
    DOI 10.1038/s41559-023-02118-5
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  4. Article ; Online: COVID-19, the first pandemic in the post-genomic era.

    van Dorp, Lucy / Houldcroft, Charlotte J / Richard, Damien / Balloux, François

    Current opinion in virology

    2021  Volume 50, Page(s) 40–48

    Abstract: The scale of the international efforts to sequence SARS-CoV-2 genomes is unprecedented. Early availability of genomes allowed rapid characterisation of the virus, thus kickstarting many highly successful vaccine development programmes. Worldwide genomic ... ...

    Abstract The scale of the international efforts to sequence SARS-CoV-2 genomes is unprecedented. Early availability of genomes allowed rapid characterisation of the virus, thus kickstarting many highly successful vaccine development programmes. Worldwide genomic resources have provided a good understanding of the pandemic, supported close monitoring of the emergence of viral genomic diversity and pinpointed those sites to prioritise for functional characterisation. Continued genomic surveillance of global viral populations will be crucial to inform the timing of vaccine updates so as to pre-empt the spread of immune escape lineages. While genome sequencing has provided us with an exceptionally powerful tool to monitor the evolution of SARS-CoV-2, there is room for further improvements in particular in the form of less heterogeneous global surveillance and tools to rapidly identify concerning viral lineages.
    MeSH term(s) COVID-19/virology ; Cell Lineage ; Evolution, Molecular ; Genome, Viral ; Humans ; Mutation ; SARS-CoV-2/genetics
    Language English
    Publishing date 2021-07-13
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2611378-8
    ISSN 1879-6265 ; 1879-6257
    ISSN (online) 1879-6265
    ISSN 1879-6257
    DOI 10.1016/j.coviro.2021.07.002
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  5. Article ; Online: Metagenomic evidence for a polymicrobial signature of sepsis.

    Tan, Cedric Chih Shen / Acman, Mislav / van Dorp, Lucy / Balloux, Francois

    Microbial genomics

    2021  Volume 7, Issue 9

    Abstract: Our understanding of the host component of sepsis has made significant progress. However, detailed study of the microorganisms causing sepsis, either as single pathogens or microbial assemblages, has received far less attention. Metagenomic data offer ... ...

    Abstract Our understanding of the host component of sepsis has made significant progress. However, detailed study of the microorganisms causing sepsis, either as single pathogens or microbial assemblages, has received far less attention. Metagenomic data offer opportunities to characterize the microbial communities found in septic and healthy individuals. In this study we apply gradient-boosted tree classifiers and a novel computational decontamination technique built upon SHapley Additive exPlanations (SHAP) to identify microbial hallmarks which discriminate blood metagenomic samples of septic patients from that of healthy individuals. Classifiers had high performance when using the read assignments to microbial genera [area under the receiver operating characteristic (AUROC=0.995)], including after removal of species 'culture-confirmed' as the cause of sepsis through clinical testing (AUROC=0.915). Models trained on single genera were inferior to those employing a polymicrobial model and we identified multiple co-occurring bacterial genera absent from healthy controls. While prevailing diagnostic paradigms seek to identify single pathogens, our results point to the involvement of a polymicrobial community in sepsis. We demonstrate the importance of the microbial component in characterising sepsis, which may offer new biological insights into the aetiology of sepsis, and ultimately support the development of clinical diagnostic or even prognostic tools.
    MeSH term(s) Bacteria/genetics ; Humans ; Machine Learning ; Metagenome ; Metagenomics ; Microbiota ; Sepsis/diagnosis ; Sepsis/microbiology
    Language English
    Publishing date 2021-09-03
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2835258-0
    ISSN 2057-5858 ; 2057-5858
    ISSN (online) 2057-5858
    ISSN 2057-5858
    DOI 10.1099/mgen.0.000642
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Population structure and hybridisation in a population of Hawaiian feral chickens.

    Martin Cerezo, Maria Luisa / López, Saioa / van Dorp, Lucy / Hellenthal, Garrett / Johnsson, Martin / Gering, Eben / Henriksen, Rie / Wright, Dominic

    Heredity

    2023  Volume 130, Issue 3, Page(s) 154–162

    Abstract: Chickens are believed to have inhabited the Hawaiian island of Kauai since the first human migrations around 1200AD, but numbers have peaked since the tropical storms Iniki and Iwa in the 1980s and 1990s that destroyed almost all the chicken coops on the ...

    Abstract Chickens are believed to have inhabited the Hawaiian island of Kauai since the first human migrations around 1200AD, but numbers have peaked since the tropical storms Iniki and Iwa in the 1980s and 1990s that destroyed almost all the chicken coops on the island and released large numbers of domestic chickens into the wild. Previous studies have shown these now feral chickens are an admixed population between Red Junglefowl (RJF) and domestic chickens. Here, using genetic haplotypic data, we estimate the time of the admixture event between the feral population on the island and the RJF to 1981 (1976-1995), coinciding with the timings of storm Iwa and Iniki. Analysis of genetic structure reveals a greater similarity between individuals inhabiting the northern and western part of the island to RJF than individuals from the eastern part of the island. These results point to the possibility of introgression events between feral chickens and the wild chickens in areas surrounding the Koke'e State Park and the Alaka'i plateau, posited as two of the major RJF reservoirs in the island. Furthermore, we have inferred haplotype blocks from pooled data to determine the most plausible source of the feral population. We identify a clear contribution from RJF and layer chickens of the White Leghorn (WL) breed. This work provides independent confirmation of the traditional hypothesis surrounding the origin of the feral populations and draws attention to the possibility of introgression of domestic alleles into the wild reservoir.
    MeSH term(s) Animals ; Humans ; Chickens/genetics ; Hawaii ; Islands ; Hybridization, Genetic ; Breeding
    Language English
    Publishing date 2023-02-01
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2423-5
    ISSN 1365-2540 ; 0018-067X
    ISSN (online) 1365-2540
    ISSN 0018-067X
    DOI 10.1038/s41437-022-00589-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Increase in antioxidant capacity associated with the successful subclone of hypervirulent carbapenem-resistant Klebsiella pneumoniae ST11-KL64.

    Wang, Ruobing / Zhang, Anru / Sun, Shijun / Yin, Guankun / Wu, Xingyu / Ding, Qi / Wang, Qi / Chen, Fengning / Wang, Shuyi / van Dorp, Lucy / Zhang, Yawei / Jin, Longyang / Wang, Xiaojuan / Balloux, Francois / Wang, Hui

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 67

    Abstract: The acquisition of exogenous mobile genetic material imposes an adaptive burden on bacteria, whereas the adaptational evolution of virulence plasmids upon entry into carbapenem-resistant Klebsiella pneumoniae (CRKP) and its impact remains unclear. To ... ...

    Abstract The acquisition of exogenous mobile genetic material imposes an adaptive burden on bacteria, whereas the adaptational evolution of virulence plasmids upon entry into carbapenem-resistant Klebsiella pneumoniae (CRKP) and its impact remains unclear. To better understand the virulence in CRKP, we characterize virulence plasmids utilizing a large genomic data containing 1219 K. pneumoniae from our long-term surveillance and publicly accessible databases. Phylogenetic evaluation unveils associations between distinct virulence plasmids and serotypes. The sub-lineage ST11-KL64 CRKP acquires a pK2044-like virulence plasmid from ST23-KL1 hypervirulent K. pneumoniae, with a 2698 bp region deletion in all ST11-KL64. The deletion is observed to regulate methionine metabolism, enhance antioxidant capacity, and further improve survival of hypervirulent CRKP in macrophages. The pK2044-like virulence plasmid discards certain sequences to enhance survival of ST11-KL64, thereby conferring an evolutionary advantage. This work contributes to multifaceted understanding of virulence and provides insight into potential causes behind low fitness costs observed in bacteria.
    MeSH term(s) Antioxidants ; Klebsiella pneumoniae/genetics ; Phylogeny ; Acclimatization ; Carbapenem-Resistant Enterobacteriaceae/genetics ; Carbapenems/pharmacology ; Anti-Bacterial Agents/pharmacology
    Chemical Substances Antioxidants ; Carbapenems ; Anti-Bacterial Agents
    Language English
    Publishing date 2024-01-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-44351-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: How Does Large-Scale Genomic Analysis Shape Our Understanding of COVID Variants in Real Time?

    van Dorp, Lucy / Shey, Muki S / Ghedin, Elodie / Michor, Franziska / Koonin, Eugene V / Hampson, Katie

    Cell systems

    2021  Volume 12, Issue 2, Page(s) 109–111

    MeSH term(s) COVID-19/genetics ; Genomics/methods ; Humans ; SARS-CoV-2/genetics
    Language English
    Publishing date 2021-01-29
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2854138-8
    ISSN 2405-4720 ; 2405-4712
    ISSN (online) 2405-4720
    ISSN 2405-4712
    DOI 10.1016/j.cels.2021.01.004
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Q&A: What are pathogens, and what have they done to and for us?

    Balloux, Francois / van Dorp, Lucy

    BMC biology

    2017  Volume 15, Issue 1, Page(s) 91

    Abstract: Microbes are found on us, within us and around us. They inhabit virtually every environment on the planet and the bacteria carried by an average human, mostly in their gut, outnumber human cells. The vast majority of microbes are harmless to us, and many ...

    Abstract Microbes are found on us, within us and around us. They inhabit virtually every environment on the planet and the bacteria carried by an average human, mostly in their gut, outnumber human cells. The vast majority of microbes are harmless to us, and many play essential roles in plant, animal and human health. Others, however, are either obligate or facultative pathogens exerting a spectrum of deleterious effects on their hosts. Infectious diseases have historically represented the most common cause of death in humans until recently, exceeding by far the toll taken by wars or famines. From the dawn of humanity and throughout history, infectious diseases have shaped human evolution, demography, migrations and history.
    MeSH term(s) Bacteria/genetics ; Bacteria/pathogenicity ; Bacterial Physiological Phenomena ; Biological Evolution ; Communicable Diseases/epidemiology ; Communicable Diseases/microbiology ; Communicable Diseases/transmission ; Genome, Bacterial ; Host Specificity ; Host-Pathogen Interactions ; Humans
    Keywords covid19
    Language English
    Publishing date 2017-10-19
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2133020-7
    ISSN 1741-7007 ; 1741-7007
    ISSN (online) 1741-7007
    ISSN 1741-7007
    DOI 10.1186/s12915-017-0433-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Large-scale network analysis captures biological features of bacterial plasmids.

    Acman, Mislav / van Dorp, Lucy / Santini, Joanne M / Balloux, Francois

    Nature communications

    2020  Volume 11, Issue 1, Page(s) 2452

    Abstract: Many bacteria can exchange genetic material through horizontal gene transfer (HGT) mediated by plasmids and plasmid-borne transposable elements. Here, we study the population structure and dynamics of over 10,000 bacterial plasmids, by quantifying their ... ...

    Abstract Many bacteria can exchange genetic material through horizontal gene transfer (HGT) mediated by plasmids and plasmid-borne transposable elements. Here, we study the population structure and dynamics of over 10,000 bacterial plasmids, by quantifying their genetic similarities and reconstructing a network based on their shared k-mer content. We use a community detection algorithm to assign plasmids into cliques, which correlate with plasmid gene content, bacterial host range, GC content, and existing classifications based on replicon and mobility (MOB) types. Further analysis of plasmid population structure allows us to uncover candidates for yet undescribed replicon genes, and to identify transposable elements as the main drivers of HGT at broad phylogenetic scales. Our work illustrates the potential of network-based analyses of the bacterial 'mobilome' and opens up the prospect of a natural, exhaustive classification framework for bacterial plasmids.
    MeSH term(s) Algorithms ; Bacteria/genetics ; Base Composition/genetics ; Databases, Genetic ; Gene Regulatory Networks ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial ; Phylogeny ; Plasmids/genetics ; Replicon/genetics
    Language English
    Publishing date 2020-05-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-020-16282-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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