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Kosoltanapiwat N, van der Hoek L, Kinsella CM, Tongshoob J, Prasittichai L, Klein M, Jebbink MF, Deijs M, Reamtong O, Boonnak K, Khongsiri W, Phadungsombat J, Tongthainan D, Tulayakul P, Yindee M. A Novel Simian Adenovirus Associating with Human Adeno-virus Species G Isolated from Long-Tailed Macaque Feces. Viruses 2023; 15:1371. [PMID: 37376670 PMCID: PMC10303043 DOI: 10.3390/v15061371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
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 (Macaca fascicularis) in Ratchaburi Province, Thailand. Putatively novel astroviruses, enteroviruses, and adenoviruses were detected and confirmed by PCR analysis of long-tailed macaque fecal samples collected from areas in four provinces, Ratchaburi, Kanchanaburi, Lopburi, and Prachuap Khiri Khan, where humans and monkeys live in proximity (total n = 187). Astroviruses, enteroviruses, and adenoviruses were present in 3.2%, 7.5%, and 4.8% of macaque fecal samples, respectively. One adenovirus, named AdV-RBR-6-3, was successfully isolated in human cell culture. Whole-genome analysis suggested that it is a new member of the species Human adenovirus G, closely related to Rhesus adenovirus 53, with evidence of genetic recombination and variation in the hexon, fiber, and CR1 genes. Sero-surveillance showed neutralizing antibodies against AdV-RBR-6-3 in 2.9% and 11.2% of monkeys and humans, respectively, suggesting cross-species infection of monkeys and humans. Overall, we reported the use of metagenomics to screen for possible new viruses, as well as the isolation and molecular and serological characterization of the new adenovirus with cross-species transmission potential. The findings emphasize that zoonotic surveillance is important and should be continued, especially in areas where humans and animals interact, to predict and prevent the threat of emerging zoonotic pathogens.
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Affiliation(s)
- Nathamon Kosoltanapiwat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.T.); (W.K.)
| | - Lia van der Hoek
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (L.v.d.H.); (C.M.K.); (M.K.); (M.F.J.); (M.D.)
| | - Cormac M. Kinsella
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (L.v.d.H.); (C.M.K.); (M.K.); (M.F.J.); (M.D.)
| | - Jarinee Tongshoob
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.T.); (W.K.)
| | - Luxsana Prasittichai
- Wildlife Conservation Division, Protected Areas Regional Office 3 (Ban Pong), Department of National Parks, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Ratchaburi 70110, Thailand;
| | - Michelle Klein
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (L.v.d.H.); (C.M.K.); (M.K.); (M.F.J.); (M.D.)
| | - Maarten F. Jebbink
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (L.v.d.H.); (C.M.K.); (M.K.); (M.F.J.); (M.D.)
| | - Martin Deijs
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (L.v.d.H.); (C.M.K.); (M.K.); (M.F.J.); (M.D.)
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Kobporn Boonnak
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;
| | - Wathusiri Khongsiri
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.T.); (W.K.)
| | - Juthamas Phadungsombat
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan;
| | - Daraka Tongthainan
- Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-ok, Chonburi 20110, Thailand;
| | - Phitsanu Tulayakul
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Kasetsart University, Nakhon Pathom 73140, Thailand;
| | - Marnoch Yindee
- Akkhraratchakumari Veterinary College, Walailak University, Nakhonsithammarat 80161, Thailand;
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2
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Kinsella CM, Edridge AWD, van Zeggeren IE, Deijs M, van de Beek D, Brouwer MC, van der Hoek L. Bacterial ribosomal RNA detection in cerebrospinal fluid using a viromics approach. Fluids Barriers CNS 2022; 19:102. [PMID: 36550487 PMCID: PMC9773461 DOI: 10.1186/s12987-022-00400-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
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.
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Affiliation(s)
- Cormac M. Kinsella
- grid.7177.60000000084992262Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,Amsterdam Institute for Infection and Immunity, Postbus 22660, 1100 DD Amsterdam, The Netherlands
| | - Arthur W. D. Edridge
- grid.7177.60000000084992262Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,Amsterdam Institute for Infection and Immunity, Postbus 22660, 1100 DD Amsterdam, The Netherlands
| | - Ingeborg E. van Zeggeren
- grid.7177.60000000084992262Amsterdam UMC, Department of Neurology, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,grid.484519.5Amsterdam Neuroscience, Neuroinfection and Inflammation, Amsterdam, The Netherlands
| | - Martin Deijs
- grid.7177.60000000084992262Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,Amsterdam Institute for Infection and Immunity, Postbus 22660, 1100 DD Amsterdam, The Netherlands
| | - Diederik van de Beek
- grid.7177.60000000084992262Amsterdam UMC, Department of Neurology, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,grid.484519.5Amsterdam Neuroscience, Neuroinfection and Inflammation, Amsterdam, The Netherlands
| | - Matthijs C. Brouwer
- grid.7177.60000000084992262Amsterdam UMC, Department of Neurology, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,grid.484519.5Amsterdam Neuroscience, Neuroinfection and Inflammation, Amsterdam, The Netherlands
| | - Lia van der Hoek
- grid.7177.60000000084992262Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,Amsterdam Institute for Infection and Immunity, Postbus 22660, 1100 DD Amsterdam, The Netherlands
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3
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Kinsella CM, Deijs M, Gittelbauer HM, van der Hoek L, van Dijk K. Human Clinical Isolates of Pathogenic Fungi Are Host to Diverse Mycoviruses. Microbiol Spectr 2022; 10:e0161022. [PMID: 35993766 PMCID: PMC9603141 DOI: 10.1128/spectrum.01610-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/08/2022] [Indexed: 12/31/2022] Open
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. IMPORTANCE Fungal pathogens of humans are a growing global health burden. Viruses of fungi may represent future therapeutic tools, but for many fungal pathogens there are no known viruses. Our study examined the viral content of diverse human-pathogenic fungi in a clinical biobank, identifying numerous viral genomes, including one lineage previously not known to infect fungi.
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Affiliation(s)
- Cormac M. Kinsella
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Martin Deijs
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - H. M. Gittelbauer
- Amsterdam UMC, Laboratory of Mycology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, The Netherlands
| | - Lia van der Hoek
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Karin van Dijk
- Amsterdam UMC, Laboratory of Mycology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, The Netherlands
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Kumar S, Kumar GS, Maitra SS, Malý P, Bharadwaj S, Sharma P, Dwivedi VD. Viral informatics: bioinformatics-based solution for managing viral infections. Brief Bioinform 2022; 23:6659740. [PMID: 35947964 DOI: 10.1093/bib/bbac326] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/26/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Several new viral infections have emerged in the human population and establishing as global pandemics. With advancements in translation research, the scientific community has developed potential therapeutics to eradicate or control certain viral infections, such as smallpox and polio, responsible for billions of disabilities and deaths in the past. Unfortunately, some viral infections, such as dengue virus (DENV) and human immunodeficiency virus-1 (HIV-1), are still prevailing due to a lack of specific therapeutics, while new pathogenic viral strains or variants are emerging because of high genetic recombination or cross-species transmission. Consequently, to combat the emerging viral infections, bioinformatics-based potential strategies have been developed for viral characterization and developing new effective therapeutics for their eradication or management. This review attempts to provide a single platform for the available wide range of bioinformatics-based approaches, including bioinformatics methods for the identification and management of emerging or evolved viral strains, genome analysis concerning the pathogenicity and epidemiological analysis, computational methods for designing the viral therapeutics, and consolidated information in the form of databases against the known pathogenic viruses. This enriched review of the generally applicable viral informatics approaches aims to provide an overview of available resources capable of carrying out the desired task and may be utilized to expand additional strategies to improve the quality of translation viral informatics research.
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Affiliation(s)
- Sanjay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Geethu S Kumar
- Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | | | - Petr Malý
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Shiv Bharadwaj
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India.,Institute of Advanced Materials, IAAM, 59053 Ulrika, Sweden
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5
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Wang H, Yang GX, Hu Y, Lam P, Sangha K, Siciliano D, Swenerton A, Miller R, Tilley P, Von Dadelszen P, Kalyan S, Tang P, Patel MS. Comprehensive human amniotic fluid metagenomics supports the sterile womb hypothesis. Sci Rep 2022; 12:6875. [PMID: 35477737 PMCID: PMC9046152 DOI: 10.1038/s41598-022-10869-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 04/04/2022] [Indexed: 11/17/2022] Open
Abstract
As metagenomic approaches for detecting infectious agents have improved, each tissue that was once thought to be sterile has been found to harbor a variety of microorganisms. Controversy still exists over the status of amniotic fluid, which is part of an immunologically privileged zone that is required to prevent maternal immune system rejection of the fetus. Due to this privilege, the exclusion of microbes has been proposed to be mandatory, leading to the sterile womb hypothesis. Since nucleic acid yields from amniotic fluid are very low, contaminating nucleic acid found in water, reagents and the laboratory environment frequently confound attempts to address this hypothesis. Here we present metagenomic criteria for microorganism detection and a metagenomic method able to be performed with small volumes of starting material, while controlling for exogenous contamination, to circumvent these and other pitfalls. We use this method to show that human mid-gestational amniotic fluid has no detectable virome or microbiome, supporting the sterile womb hypothesis.
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Affiliation(s)
- HanChen Wang
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Department of Physiology, McGill University, Montreal, QC, Canada
| | - Gui Xiang Yang
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Yuxiang Hu
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada.,CureImmune Therapeutics Inc., Vancouver, BC, Canada
| | - Patricia Lam
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
| | - Karan Sangha
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Dawn Siciliano
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Anne Swenerton
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Ruth Miller
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Centre for Disease Control, Vancouver, BC, Canada.,Contextual Genomics Inc., Vancouver, BC, Canada
| | - Peter Tilley
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | - Peter Von Dadelszen
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada.,Department of Women and Children's Health, School of Life Course Sciences, King's College London, London, UK
| | - Shirin Kalyan
- Division of Endocrinology and Metabolism, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Patrick Tang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Centre for Disease Control, Vancouver, BC, Canada.,Department of Pathology, Sidra Medical and Research Center, Doha, Qatar
| | - Millan S Patel
- BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada. .,Department of Medical Genetics, University of British Columbia, 4500 Oak St., Rm. C234, Vancouver, BC, V6H 3N1, Canada.
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6
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Edridge AWD, Abd-Elfarag G, Deijs M, Jebbink MF, Boele van Hensbroek M, van der Hoek L. Divergent Rhabdovirus Discovered in a Patient with New-Onset Nodding Syndrome. Viruses 2022; 14:v14020210. [PMID: 35215803 PMCID: PMC8880091 DOI: 10.3390/v14020210] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 12/15/2022] Open
Abstract
A divergent rhabdovirus was discovered in the bloodstream of a 15-year-old girl with Nodding syndrome from Mundri West County in South Sudan. Nodding syndrome is a progressive degenerative neuropathy of unknown cause affecting thousands of individuals in Sub-Saharan Africa. The index case was previously healthy until she developed head-nodding seizures four months prior to presentation. Virus discovery by VIDISCA-NGS on the patient’s plasma detected multiple sequence reads belonging to a divergent rhabdovirus. The viral load was 3.85 × 103 copies/mL in the patient’s plasma and undetectable in her cerebrospinal fluid. Further genome walking allowed for the characterization of full coding sequences of all the viral proteins (N, P, M, U1, U2, G, U3, and L). We tentatively named the virus “Mundri virus” (MUNV) and classified it as a novel virus species based on the high divergence from other known viruses (all proteins had less than 43% amino acid identity). Phylogenetic analysis revealed that MUNV forms a monophyletic clade with several human-infecting tibroviruses prevalent in Central Africa. A bioinformatic machine-learning algorithm predicted MUNV to be an arbovirus (bagged prediction strength (BPS) of 0.9) transmitted by midges (BPS 0.4) with an artiodactyl host reservoir (BPS 0.9). An association between MUNV infection and Nodding syndrome was evaluated in a case–control study of 72 patients with Nodding syndrome (including the index case) matched to 65 healthy households and 48 community controls. No subject, besides the index case, was positive for MUNV RNA in their plasma. A serological assay detecting MUNV anti-nucleocapsid found, respectively, in 28%, 22%, and 16% of cases, household controls and community controls to be seropositive with no significant differences between cases and either control group. This suggests that MUNV commonly infects children in South Sudan yet may not be causally associated with Nodding syndrome.
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Affiliation(s)
- Arthur W. D. Edridge
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.D.); (M.F.J.)
- Center for Global Child Health, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (G.A.-E.); (M.B.v.H.)
- Correspondence: (A.W.D.E.); (L.v.d.H.)
| | - Gasim Abd-Elfarag
- Center for Global Child Health, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (G.A.-E.); (M.B.v.H.)
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.D.); (M.F.J.)
| | - Maarten F. Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.D.); (M.F.J.)
| | - Michael Boele van Hensbroek
- Center for Global Child Health, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (G.A.-E.); (M.B.v.H.)
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.D.); (M.F.J.)
- Correspondence: (A.W.D.E.); (L.v.d.H.)
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7
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Dynamics of the Enteric Virome in a Swine Herd Affected by Non-PCV2/PRRSV Postweaning Wasting Syndrome. Viruses 2021; 13:v13122538. [PMID: 34960807 PMCID: PMC8705478 DOI: 10.3390/v13122538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/13/2021] [Indexed: 12/24/2022] Open
Abstract
A commercial pig farm with no history of porcine circovirus 2 (PCV2) or porcine reproductive and respiratory syndrome virus (PRRSV) repeatedly reported a significant reduction in body weight gain and wasting symptoms in approximately 20–30% of the pigs in the period between three and six weeks after weaning. As standard clinical interventions failed to tackle symptomatology, viral metagenomics were used to describe and monitor the enteric virome at birth, 3 weeks, 4 weeks, 6 weeks, and 9 weeks of age. The latter four sampling points were 7 days, 3 weeks, and 6 weeks post weaning, respectively. Fourteen distinct enteric viruses were identified within the herd, which all have previously been linked to enteric diseases. Here we show that wasting is associated with alterations in the enteric virome of the pigs, characterized by: (1) the presence of enterovirus G at 3 weeks of age, followed by a higher prevalence of the virus in wasting pigs at 6 weeks after weaning; (2) rotaviruses at 3 weeks of age; and (3) porcine sapovirus one week after weaning. However, the data do not provide a causal link between specific viral infections and the postweaning clinical problems on the farm. Together, our results offer evidence that disturbances in the enteric virome at the preweaning stage and early after weaning have a determining role in the development of intestinal barrier dysfunctions and nutrient uptake in the postweaning growth phase. Moreover, we show that the enteric viral load sharply increases in the week after weaning in both healthy and wasting pigs. This study is also the first to report the dynamics and co-infection of porcine rotavirus species and porcine astrovirus genetic lineages during the first 9 weeks of the life of domestic pigs.
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8
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van Lieverloo GGA, Wieske L, van Schaik IN, Deijs M, van der Hoek L, Eftimov F. Virus discovery in chronic inflammatory demyelinating polyneuropathy. J Neuroimmunol 2021; 358:577668. [PMID: 34325344 DOI: 10.1016/j.jneuroim.2021.577668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/22/2021] [Accepted: 07/18/2021] [Indexed: 11/18/2022]
Abstract
The events triggering and/or sustaining the auto-immune response underlying chronic inflammatory demyelinating polyneuropathy (CIDP) are unknown. Similar to Guillain-Barré syndrome (GBS), a viral infection might play a role in CIDP. In this study, an virus detection method (VIDISCA-next generation sequencing) capable of detecting known and unknown viruses, was used to analyze the virome in serum of 47 CIDP patients at different time points of the disease and, when available, in cerebrospinal fluid (CSF) samples (N: 17). Serum samples of GBS patients (N:24) and healthy controls (N:114) were used for comparisons. In 5/47 (10.6%; 95% CI: 4-23) CIDP samples, 10/24 (42%; 95% CI: 22-63) GBS samples and 32/114 (28.1%; 95% CI: 20-37) healthy controls samples, anelloviruses were detected, generally regarded as a non-pathogenic species. Parvovirus B19 and GB virus C were found in two CIDP samples (4%). Parvovirus B19, HIV-1 and GB virus C were found in three GBS samples (13%). In 2/17 CIDP CSF samples, an anellovirus and polyomavirus were detected, probably due to contamination during lumbar puncture. No sequences of other viruses were detected in serum or CSF. A (persistent) viral infection sustaining the auto-immune response in CIDP seems therefore unlikely.
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Affiliation(s)
| | - L Wieske
- Amsterdam UMC, Department of Neurology, Amsterdam, the Netherlands
| | - I N van Schaik
- Amsterdam UMC, Department of Neurology, Amsterdam, the Netherlands; Spaarne Gasthuis, Haarlem, the Netherlands
| | - M Deijs
- Amsterdam UMC, Laboratory of Experimental Virology, Amsterdam, the Netherlands
| | - L van der Hoek
- Amsterdam UMC, Laboratory of Experimental Virology, Amsterdam, the Netherlands
| | - F Eftimov
- Amsterdam UMC, Department of Neurology, Amsterdam, the Netherlands
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9
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Mugimba KK, Byarugaba DK, Mutoloki S, Evensen Ø, Munang’andu HM. Challenges and Solutions to Viral Diseases of Finfish in Marine Aquaculture. Pathogens 2021; 10:pathogens10060673. [PMID: 34070735 PMCID: PMC8227678 DOI: 10.3390/pathogens10060673] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
Aquaculture is the fastest food-producing sector in the world, accounting for one-third of global food production. As is the case with all intensive farming systems, increase in infectious diseases has adversely impacted the growth of marine fish farming worldwide. Viral diseases cause high economic losses in marine aquaculture. We provide an overview of the major challenges limiting the control and prevention of viral diseases in marine fish farming, as well as highlight potential solutions. The major challenges include increase in the number of emerging viral diseases, wild reservoirs, migratory species, anthropogenic activities, limitations in diagnostic tools and expertise, transportation of virus contaminated ballast water, and international trade. The proposed solutions to these problems include developing biosecurity policies at global and national levels, implementation of biosecurity measures, vaccine development, use of antiviral drugs and probiotics to combat viral infections, selective breeding of disease-resistant fish, use of improved diagnostic tools, disease surveillance, as well as promoting the use of good husbandry and management practices. A multifaceted approach combining several control strategies would provide more effective long-lasting solutions to reduction in viral infections in marine aquaculture than using a single disease control approach like vaccination alone.
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Affiliation(s)
- Kizito K. Mugimba
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala P.O. Box 7062, Uganda;
- Correspondence: (K.K.M.); (H.M.M.); Tel.: +256-772-56-7940 (K.K.M.); +47-98-86-86-83 (H.M.M.)
| | - Denis K. Byarugaba
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala P.O. Box 7062, Uganda;
| | - Stephen Mutoloki
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 369, 0102 Oslo, Norway; (S.M.); (Ø.E.)
| | - Øystein Evensen
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 369, 0102 Oslo, Norway; (S.M.); (Ø.E.)
| | - Hetron M. Munang’andu
- Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 369, 0102 Oslo, Norway
- Correspondence: (K.K.M.); (H.M.M.); Tel.: +256-772-56-7940 (K.K.M.); +47-98-86-86-83 (H.M.M.)
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10
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Folgueiras-González A, van den Braak R, Deijs M, van der Hoek L, de Groof A. A Versatile Processing Workflow to Enable Pathogen Detection in Clinical Samples from Organs Using VIDISCA. Diagnostics (Basel) 2021; 11:diagnostics11050791. [PMID: 33925752 PMCID: PMC8145099 DOI: 10.3390/diagnostics11050791] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/16/2021] [Accepted: 04/26/2021] [Indexed: 12/15/2022] Open
Abstract
In recent years, refined molecular methods coupled with powerful high throughput sequencing technologies have increased the potential of virus discovery in clinical samples. However, host genetic material remains a complicating factor that interferes with discovery of novel viruses in solid tissue samples as the relative abundance of the virus material is low. Physical enrichment processing methods, although usually complicated, labor-intensive, and costly, have proven to be successful for improving sensitivity of virus detection in complex samples. In order to further increase detectability, we studied the application of fast and simple high-throughput virus enrichment methods on tissue homogenates. Probe sonication in high EDTA concentrations, organic extraction with Vertrel™ XF, or a combination of both, were applied prior to chromatography-like enrichment using Capto™ Core 700 resin, after which effects on virus detection sensitivity by the VIDISCA method were determined. Sonication in the presence of high concentrations of EDTA showed the best performance with an increased proportion of viral reads, up to 9.4 times, yet minimal effect on the host background signal. When this sonication procedure in high EDTA concentrations was followed by organic extraction with Vertrel™ XF and two rounds of core bead chromatography enrichment, an increase up to 10.5 times in the proportion of viral reads in the processed samples was achieved, with reduction of host background sequencing. We present a simple and semi-high-throughput method that can be used to enrich homogenized tissue samples for viral reads.
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Affiliation(s)
- Alba Folgueiras-González
- Department Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands; (A.F.-G.); (R.v.d.B.)
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.D.); (L.v.d.H.)
| | - Robin van den Braak
- Department Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands; (A.F.-G.); (R.v.d.B.)
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.D.); (L.v.d.H.)
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.D.); (L.v.d.H.)
| | - Ad de Groof
- Department Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands; (A.F.-G.); (R.v.d.B.)
- Correspondence:
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11
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Diagnostic accuracy of VIDISCA-NGS in patients with suspected central nervous system infections. Clin Microbiol Infect 2021; 27:631.e7-631.e12. [DOI: 10.1016/j.cmi.2020.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 01/09/2023]
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12
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Integrative Transkingdom Analysis of the Gut Microbiome in Antibiotic Perturbation and Critical Illness. mSystems 2021; 6:6/2/e01148-20. [PMID: 33727397 PMCID: PMC8546997 DOI: 10.1128/msystems.01148-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Bacterial microbiota play a critical role in mediating local and systemic immunity, and shifts in these microbial communities have been linked to impaired outcomes in critical illness. Emerging data indicate that other intestinal organisms, including bacteriophages, viruses of eukaryotes, fungi, and protozoa, are closely interlinked with the bacterial microbiota and their host, yet their collective role during antibiotic perturbation and critical illness remains to be elucidated. We employed multi-omics factor analysis (MOFA) to systematically integrate the bacterial (16S rRNA), fungal (intergenic transcribed spacer 1 rRNA), and viral (virus discovery next-generation sequencing) components of the intestinal microbiota of 33 critically ill patients with and without sepsis and 13 healthy volunteers. In addition, we quantified the absolute abundances of bacteria and fungi using 16S and 18S rRNA PCRs and characterized the short-chain fatty acids (SCFAs) butyrate, acetate, and propionate using nuclear magnetic resonance spectroscopy. We observe that a loss of the anaerobic intestinal environment is directly correlated with an overgrowth of aerobic pathobionts and their corresponding bacteriophages as well as an absolute enrichment of opportunistic yeasts capable of causing invasive disease. We also observed a strong depletion of SCFAs in both disease states, which was associated with an increased absolute abundance of fungi with respect to bacteria. Therefore, these findings illustrate the complexity of transkingdom changes following disruption of the intestinal bacterial microbiome. IMPORTANCE While numerous studies have characterized antibiotic-induced disruptions of the bacterial microbiome, few studies describe how these disruptions impact the composition of other kingdoms such as viruses, fungi, and protozoa. To address this knowledge gap, we employed MOFA to systematically integrate viral, fungal, and bacterial sequence data from critically ill patients (with and without sepsis) and healthy volunteers, both prior to and following exposure to broad-spectrum antibiotics. In doing so, we show that modulation of the bacterial component of the microbiome has implications extending beyond this kingdom alone, enabling the overgrowth of potentially invasive fungi and viruses. While numerous preclinical studies have described similar findings in vitro, we confirm these observations in humans using an integrative analytic approach. These findings underscore the potential value of multi-omics data integration tools in interrogating how different components of the microbiota contribute to disease states. In addition, our findings suggest that there is value in further studying potential adjunctive therapies using anaerobic bacteria or SCFAs to reduce fungal expansion after antibiotic exposure, which could ultimately lead to improved outcomes in the intensive care unit (ICU).
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13
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Kinsella CM, Bart A, Deijs M, Broekhuizen P, Kaczorowska J, Jebbink MF, van Gool T, Cotten M, van der Hoek L. Entamoeba and Giardia parasites implicated as hosts of CRESS viruses. Nat Commun 2020; 11:4620. [PMID: 32934242 PMCID: PMC7493932 DOI: 10.1038/s41467-020-18474-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 08/25/2020] [Indexed: 12/13/2022] Open
Abstract
Metagenomic techniques have enabled genome sequencing of unknown viruses without isolation in cell culture, but information on the virus host is often lacking, preventing viral characterisation. High-throughput methods capable of identifying virus hosts based on genomic data alone would aid evaluation of their medical or biological relevance. Here, we address this by linking metagenomic discovery of three virus families in human stool samples with determination of probable hosts. Recombination between viruses provides evidence of a shared host, in which genetic exchange occurs. We utilise networks of viral recombination to delimit virus-host clusters, which are then anchored to specific hosts using (1) statistical association to a host organism in clinical samples, (2) endogenous viral elements in host genomes, and (3) evidence of host small RNA responses to these elements. This analysis suggests two CRESS virus families (Naryaviridae and Nenyaviridae) infect Entamoeba parasites, while a third (Vilyaviridae) infects Giardia duodenalis. The trio supplements five CRESS virus families already known to infect eukaryotes, extending the CRESS virus host range to protozoa. Phylogenetic analysis implies CRESS viruses infecting multicellular life have evolved independently on at least three occasions.
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Affiliation(s)
- Cormac M Kinsella
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
| | - Aldert Bart
- Laboratory of Clinical Parasitology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Patricia Broekhuizen
- Laboratory of Clinical Parasitology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Joanna Kaczorowska
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Maarten F Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Tom van Gool
- Laboratory of Clinical Parasitology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Matthew Cotten
- MRC/UVRI & LSHTM Uganda Research Unit, 3FC6+Q3, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, G61 1QH, Glasgow, UK
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
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14
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Dávila-Ramos S, Castelán-Sánchez HG, Martínez-Ávila L, Sánchez-Carbente MDR, Peralta R, Hernández-Mendoza A, Dobson ADW, Gonzalez RA, Pastor N, Batista-García RA. A Review on Viral Metagenomics in Extreme Environments. Front Microbiol 2019; 10:2403. [PMID: 31749771 PMCID: PMC6842933 DOI: 10.3389/fmicb.2019.02403] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/04/2019] [Indexed: 12/22/2022] Open
Abstract
Viruses are the most abundant biological entities in the biosphere, and have the ability to infect Bacteria, Archaea, and Eukaryotes. The virome is estimated to be at least ten times more abundant than the microbiome with 107 viruses per milliliter and 109 viral particles per gram in marine waters and sediments or soils, respectively. Viruses represent a largely unexplored genetic diversity, having an important role in the genomic plasticity of their hosts. Moreover, they also play a significant role in the dynamics of microbial populations. In recent years, metagenomic approaches have gained increasing popularity in the study of environmental viromes, offering the possibility of extending our knowledge related to both virus diversity and their functional characterization. Extreme environments represent an interesting source of both microbiota and their virome due to their particular physicochemical conditions, such as very high or very low temperatures and >1 atm hydrostatic pressures, among others. Despite the fact that some progress has been made in our understanding of the ecology of the microbiota in these habitats, few metagenomic studies have described the viromes present in extreme ecosystems. Thus, limited advances have been made in our understanding of the virus community structure in extremophilic ecosystems, as well as in their biotechnological potential. In this review, we critically analyze recent progress in metagenomic based approaches to explore the viromes in extreme environments and we discuss the potential for new discoveries, as well as methodological challenges and perspectives.
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Affiliation(s)
- Sonia Dávila-Ramos
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Hugo G. Castelán-Sánchez
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Liliana Martínez-Ávila
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | | | - Raúl Peralta
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Armando Hernández-Mendoza
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
| | - Ramón A. Gonzalez
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
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15
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Edridge AWD, Deijs M, van Zeggeren IE, Kinsella CM, Jebbink MF, Bakker M, van de Beek D, Brouwer MC, van der Hoek L. Viral Metagenomics on Cerebrospinal Fluid. Genes (Basel) 2019; 10:E332. [PMID: 31052348 PMCID: PMC6562652 DOI: 10.3390/genes10050332] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/23/2019] [Accepted: 04/24/2019] [Indexed: 02/07/2023] Open
Abstract
Identifying the causative pathogen in central nervous system (CNS) infections is crucial for patient management and prognosis. Many viruses can cause CNS infections, yet screening for each individually is costly and time-consuming. Most metagenomic assays can theoretically detect all pathogens, but often fail to detect viruses because of their small genome and low viral load. Viral metagenomics overcomes this by enrichment of the viral genomic content in a sample. VIDISCA-NGS is one of the available workflows for viral metagenomics, which requires only a small input volume and allows multiplexing of multiple samples per run. The performance of VIDISCA-NGS was tested on 45 cerebrospinal fluid (CSF) samples from patients with suspected CNS infections in which a virus was identified and quantified by polymerase chain reaction. Eighteen were positive for an RNA virus, and 34 for a herpesvirus. VIDISCA-NGS detected all RNA viruses with a viral load >2 × 104 RNA copies/mL (n = 6) and 8 of 12 of the remaining low load samples. Only one herpesvirus was identified by VIDISCA-NGS, however, when withholding a DNase treatment, 11 of 18 samples with a herpesvirus load >104 DNA copies/mL were detected. Our results indicate that VIDISCA-NGS has the capacity to detect low load RNA viruses in CSF. Herpesvirus DNA in clinical samples is probably non-encapsidated and therefore difficult to detect by VIDISCA-NGS.
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Affiliation(s)
- Arthur W D Edridge
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Ingeborg E van Zeggeren
- Department of Neurology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, 1105 AZ Amsterdam, The Netherlands.
| | - Cormac M Kinsella
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Maarten F Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Diederik van de Beek
- Department of Neurology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, 1105 AZ Amsterdam, The Netherlands.
| | - Matthijs C Brouwer
- Department of Neurology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, 1105 AZ Amsterdam, The Netherlands.
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
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