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Article ; Online: Vertebrate-tropism of a cressdnavirus lineage implicated by poxvirus gene capture.

Kinsella, Cormac M / van der Hoek, Lia

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

2023 Volume 120, Issue 20, Page(s) e2303844120

Abstract: Among cressdnaviruses, only the ... ...

Abstract	Among cressdnaviruses, only the family
MeSH term(s)	Animals ; Phylogeny ; Poxviridae/genetics ; Avipoxvirus/genetics ; Birds ; Tropism
Language	English
Publishing date	2023-05-08
Publishing country	United States
Document type	Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2303844120
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Anellovirus evolution during long-term chronic infection.

Kaczorowska, Joanna / Timmerman, Anne L / Deijs, Martin / Kinsella, Cormac M / Bakker, Margreet / van der Hoek, Lia

Virus evolution

2023 Volume 9, Issue 1, Page(s) vead001

Abstract: Human anelloviruses (AVs) are extremely genetically diverse, are widespread in the human population, and cause chronic infections. However, the evolutionary dynamics of AVs within single hosts is currently unknown, and it is unclear whether these changes ...

Abstract	Human anelloviruses (AVs) are extremely genetically diverse, are widespread in the human population, and cause chronic infections. However, the evolutionary dynamics of AVs within single hosts is currently unknown, and it is unclear whether these changes have an implication on the long-term persistence of AVs in the host. Here, we assessed the evolutionary dynamics of six AV lineages during 30 years of chronic infection at single host resolution. The total number of substitutions and the number of variable sites increased over time. However, not all substitutions reached population fixation, showing that AV lineages form heterogeneous swarms within the host. Most substitutions occurred within a hypervariable region (HVR) located between nucleotide positions 800 and 1,300 of
Language	English
Publishing date	2023-01-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2818949-8
ISSN	2057-1577
ISSN	2057-1577
DOI	10.1093/ve/vead001
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Article ; Online: Correction: Kosoltanapiwat et al. A Novel Simian Adenovirus Associating with Human Adenovirus Species G Isolated from Long-Tailed Macaque Feces.

Kosoltanapiwat, Nathamon / van der Hoek, Lia / Kinsella, Cormac M / Tongshoob, Jarinee / Prasittichai, Luxsana / Klein, Michelle / Jebbink, Maarten F / Deijs, Martin / Reamtong, Onrapak / Boonnak, Kobporn / Khongsiri, Wathusiri / Phadungsombat, Juthamas / Tongthainan, Daraka / Tulayakul, Phitsanu / Yindee, Marnoch

Viruses

2023 Volume 15, Issue 9

Abstract: After publication of the article, the authors received comments from a member of ... ...

Abstract	After publication of the article, the authors received comments from a member of the
Language	English
Publishing date	2023-09-04
Publishing country	Switzerland
Document type	Published Erratum
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15091871
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Human Clinical Isolates of Pathogenic Fungi Are Host to Diverse Mycoviruses.

Kinsella, Cormac M / Deijs, Martin / Gittelbauer, H M / van der Hoek, Lia / van Dijk, Karin

Microbiology spectrum

2022 Volume 10, Issue 5, Page(s) e0161022

Abstract: Fungi host viruses from many families, and next-generation sequencing can be used to discover previously unknown genomes. Some fungus-infecting viruses (mycoviruses) confer hypovirulence on their pathogenic hosts, raising the possibility of therapeutic ... ...

Abstract	Fungi host viruses from many families, and next-generation sequencing can be used to discover previously unknown genomes. Some fungus-infecting viruses (mycoviruses) confer hypovirulence on their pathogenic hosts, raising the possibility of therapeutic application in the treatment of fungal diseases. Though all fungi probably host mycoviruses, many human pathogens have none documented, implying the mycoviral catalogue remains at an early stage. Here, we carried out virus discovery on 61 cultures of pathogenic fungi covering 27 genera and at least 56 species. Using next-generation sequencing of total nucleic acids, we found no DNA viruses but did find a surprising RNA virus diversity of 11 genomes from six classified families and two unclassified lineages, including eight genomes likely representing new species. Among these was the first jivivirus detected in a fungal host (Aspergillus lentulus). We separately utilized rolling circle amplification and next-generation sequencing to identify ssDNA viruses specifically. We identified 13 new cressdnaviruses across all libraries, but unlike the RNA viruses, they could not be confirmed by PCR in either the original unamplified samples or freshly amplified nucleic acids. Their distributions among sequencing libraries and inconsistent detection suggest low-level contamination of reagents. This highlights both the importance of validation assays and the risks of viral host prediction on the basis of highly amplified sequencing libraries. Meanwhile, the detected RNA viruses provide a basis for experimentation to characterize possible hypovirulent effects, and hint at a wealth of uncharted viral diversity currently frozen in biobanks.
MeSH term(s)	Humans ; Fungal Viruses/genetics ; RNA Viruses ; Fungi/genetics ; Genome, Viral ; Nucleic Acids ; Phylogeny
Chemical Substances	Nucleic Acids
Language	English
Publishing date	2022-08-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.01610-22
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Host prediction for disease-associated gastrointestinal cressdnaviruses.

Kinsella, Cormac M / Deijs, Martin / Becker, Christin / Broekhuizen, Patricia / van Gool, Tom / Bart, Aldert / Schaefer, Arne S / van der Hoek, Lia

Virus evolution

2022 Volume 8, Issue 2, Page(s) veac087

Abstract: Metagenomic techniques have facilitated the discovery of thousands of viruses, yet because samples are often highly biodiverse, fundamental data on the specific cellular hosts are usually missing. Numerous gastrointestinal viruses linked to human or ... ...

Abstract	Metagenomic techniques have facilitated the discovery of thousands of viruses, yet because samples are often highly biodiverse, fundamental data on the specific cellular hosts are usually missing. Numerous gastrointestinal viruses linked to human or animal diseases are affected by this, preventing research into their medical or veterinary importance. Here, we developed a computational workflow for the prediction of viral hosts from complex metagenomic datasets. We applied it to seven lineages of gastrointestinal cressdnaviruses using 1,124 metagenomic datasets, predicting hosts of four lineages. The
Language	English
Publishing date	2022-09-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2818949-8
ISSN	2057-1577
ISSN	2057-1577
DOI	10.1093/ve/veac087
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Article ; Online: Diversity and Long-Term Dynamics of Human Blood Anelloviruses.

Kaczorowska, Joanna / Deijs, Martin / Klein, Michelle / Bakker, Margreet / Jebbink, Maarten F / Sparreboom, Mila / Kinsella, Cormac M / Timmerman, Anne L / van der Hoek, Lia

Journal of virology

2022 Volume 96, Issue 11, Page(s) e0010922

Abstract: Anelloviruses (AVs) are commensal members of the human blood virome. Even though it was estimated that over 90% of the human population carries AVs, the dynamics of the AV virome ("anellome") are unknown. We investigated the dynamics of blood anellomes ... ...

Abstract	Anelloviruses (AVs) are commensal members of the human blood virome. Even though it was estimated that over 90% of the human population carries AVs, the dynamics of the AV virome ("anellome") are unknown. We investigated the dynamics of blood anellomes in two healthy people followed up for more than 30 years. Both subjects were positive for AVs in the majority of samples.
MeSH term(s)	Anelloviridae/classification ; Anelloviridae/genetics ; Blood/virology ; DNA Virus Infections ; DNA, Viral ; Humans ; Phylogeny ; Torque teno virus/genetics ; Virome
Chemical Substances	DNA, Viral
Language	English
Publishing date	2022-05-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/jvi.00109-22
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 609: Show issues

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Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: A Novel Simian Adenovirus Associating with Human Adeno-virus Species G Isolated from Long-Tailed Macaque Feces.

Viruses

2023 Volume 15, Issue 6

Abstract: Metagenomics has demonstrated its capability in outbreak investigations and pathogen surveillance and discovery. With high-throughput and effective bioinformatics, many disease-causing agents, as well as novel viruses of humans and animals, have been ... ...

Abstract	Metagenomics has demonstrated its capability in outbreak investigations and pathogen surveillance and discovery. With high-throughput and effective bioinformatics, many disease-causing agents, as well as novel viruses of humans and animals, have been identified using metagenomic analysis. In this study, a VIDISCA metagenomics workflow was used to identify potential unknown viruses in 33 fecal samples from asymptomatic long-tailed macaques (
MeSH term(s)	Animals ; Humans ; Macaca fascicularis ; Adenoviruses, Simian/genetics ; Thailand/epidemiology ; Macaca mulatta ; Adenoviridae ; Adenoviridae Infections/veterinary ; Enterovirus ; Enterovirus Infections ; Feces ; Phylogeny
Language	English
Publishing date	2023-06-14
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15061371
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Article ; Online: Bacterial ribosomal RNA detection in cerebrospinal fluid using a viromics approach.

Kinsella, Cormac M / Edridge, Arthur W D / van Zeggeren, Ingeborg E / Deijs, Martin / van de Beek, Diederik / Brouwer, Matthijs C / van der Hoek, Lia

Fluids and barriers of the CNS

2022 Volume 19, Issue 1, Page(s) 102

Abstract: Background: In patients with central nervous system (CNS) infections identification of the causative pathogen is important for treatment. Metagenomic next-generation sequencing techniques are increasingly being applied to identify causes of CNS ... ...

Abstract	Background: In patients with central nervous system (CNS) infections identification of the causative pathogen is important for treatment. Metagenomic next-generation sequencing techniques are increasingly being applied to identify causes of CNS infections, as they can detect any pathogen nucleic acid sequences present. Viromic techniques that enrich samples for virus particles prior to sequencing may simultaneously enrich ribosomes from bacterial pathogens, which are similar in size to small viruses. Methods: We studied the performance of a viromic library preparation technique (VIDISCA) combined with low-depth IonTorrent sequencing (median ~ 25,000 reads per sample) for detection of ribosomal RNA from common pathogens, analyzing 89 cerebrospinal fluid samples from patients with culture proven bacterial meningitis. Results: Sensitivity and specificity to Streptococcus pneumoniae (n = 24) before and after optimizing threshold parameters were 79% and 52%, then 88% and 90%. Corresponding values for Neisseria meningitidis (n = 22) were 73% and 93%, then 67% and 100%, Listeria monocytogenes (n = 24) 21% and 100%, then 27% and 100%, and Haemophilus influenzae (n = 18) 56% and 100%, then 71% and 100%. A higher total sequencing depth, no antibiotic treatment prior to lumbar puncture, increased disease severity, and higher c-reactive protein levels were associated with pathogen detection. Conclusion: We provide proof of principle that a viromic approach can be used to correctly identify bacterial ribosomal RNA in patients with bacterial meningitis. Further work should focus on increasing assay sensitivity, especially for problematic species (e.g. L. monocytogenes), as well as profiling additional pathogens. The technique is most suited to research settings and examination of idiopathic cases, rather than an acute clinical setting.
Language	English
Publishing date	2022-12-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2595406-4
ISSN	2045-8118 ; 2045-8118
ISSN (online)	2045-8118
ISSN	2045-8118
DOI	10.1186/s12987-022-00400-5
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Article ; Online: Enhanced bioinformatic profiling of VIDISCA libraries for virus detection and discovery.

Kinsella, Cormac M / Deijs, Martin / van der Hoek, Lia

Virus research

2018 Volume 263, Page(s) 21–26

Abstract: VIDISCA is a next-generation sequencing (NGS) library preparation method designed to enrich viral nucleic acids from samples before highly-multiplexed low depth sequencing. Reliable detection of known viruses and discovery of novel divergent viruses from ...

Abstract	VIDISCA is a next-generation sequencing (NGS) library preparation method designed to enrich viral nucleic acids from samples before highly-multiplexed low depth sequencing. Reliable detection of known viruses and discovery of novel divergent viruses from NGS data require dedicated analysis tools that are both sensitive and accurate. Existing software was utilised to design a new bioinformatic workflow for high-throughput detection and discovery of viruses from VIDISCA data. The workflow leverages the VIDISCA library preparation molecular biology, specifically the use of Mse1 restriction enzyme which produces biological replicate library inserts from identical genomes. The workflow performs total metagenomic analysis for classification of non-viral sequence including parasites and host, and separately carries out virus specific analyses. Ribosomal RNA sequence is removed to increase downstream analysis speed and remaining reads are clustered at 100% identity. Known and novel viruses are sensitively detected via alignment to a virus-only protein database, and false positives are removed. A new cluster-profiling analysis takes advantage of the viral biological replicates produced by Mse1 digestion, using read clustering to flag the presence of short genomes at very high copy number. Importantly, this analysis ensures that highly repeated sequences are identified even if no homology is detected, as is shown here with the detection of a novel gokushovirus genome from human faecal matter. The workflow was validated using read data derived from serum and faeces samples taken from HIV-1 positive adults, and serum samples from pigs that were infected with atypical porcine pestivirus.
MeSH term(s)	Algorithms ; Animals ; Blood/virology ; Computational Biology/methods ; Feces/virology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; Swine ; Viruses/genetics ; Viruses/isolation & purification
Language	English
Publishing date	2018-12-19
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Validation Studies
ZDB-ID	605780-9
ISSN	1872-7492 ; 0168-1702
ISSN (online)	1872-7492
ISSN	0168-1702
DOI	10.1016/j.virusres.2018.12.010
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Zs.A 1965: Show issues

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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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Article ; Online: Entamoeba and Giardia parasites implicated as hosts of CRESS viruses

Cormac M. Kinsella / Aldert Bart / Martin Deijs / Patricia Broekhuizen / Joanna Kaczorowska / Maarten F. Jebbink / Tom van Gool / Matthew Cotten / Lia van der Hoek

Nature Communications, Vol 11, Iss 1, Pp 1-

2020 Volume 10

Abstract: ... Kinsella et al. use recombination events between virus genomes, statistical association of viruses to hosts ...

Abstract	Metagenomics allows virus genome discovery, but the viral hosts are often not identified. Here, Kinsella et al. use recombination events between virus genomes, statistical association of viruses to hosts in clinical samples, and analysis of endogenous viral elements in host genomes to identify probable hosts of three CRESS virus families.
Keywords	Science ; Q
Language	English
Publishing date	2020-09-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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