1
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Lopez-Labrador FX, Huber M, Sidorov IA, Brown JR, Cuypers L, Laenen L, Vanmechelen B, Maes P, Fischer N, Pichler I, Storey N, Atkinson L, Schmutz S, Kufner V, van Boheemen S, Mulders CE, Grundhoff A, Blümke P, Robitaille A, Cinek O, Hubáčková K, Mourik K, Boers SA, Stauber L, Salmona M, Cappy P, Ramette A, Franze' A, LeGoff J, Claas ECJ, Rodriguez C, de Vries JJC. Multicenter benchmarking of short and long read wet lab protocols for clinical viral metagenomics. J Clin Virol 2024; 173:105695. [PMID: 38823290 DOI: 10.1016/j.jcv.2024.105695] [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: 01/13/2024] [Revised: 04/10/2024] [Accepted: 05/18/2024] [Indexed: 06/03/2024]
Abstract
Metagenomics is gradually being implemented for diagnosing infectious diseases. However, in-depth protocol comparisons for viral detection have been limited to individual sets of experimental workflows and laboratories. In this study, we present a benchmark of metagenomics protocols used in clinical diagnostic laboratories initiated by the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS). A mock viral reference panel was designed to mimic low biomass clinical specimens. The panel was used to assess the performance of twelve metagenomic wet lab protocols currently in use in the diagnostic laboratories of participating ENNGS member institutions. Both Illumina and Nanopore, shotgun and targeted capture probe protocols were included. Performance metrics sensitivity, specificity, and quantitative potential were assessed using a central bioinformatics pipeline. Overall, viral pathogens with loads down to 104 copies/ml (corresponding to CT values of 31 in our PCR assays) were detected by all the evaluated metagenomic wet lab protocols. In contrast, lower abundant mixed viruses of CT values of 35 and higher were detected only by a minority of the protocols. Considering the reference panel as the gold standard, optimal thresholds to define a positive result were determined per protocol, based on the horizontal genome coverage. Implementing these thresholds, sensitivity and specificity of the protocols ranged from 67 to 100 % and 87 to 100 %, respectively. A variety of metagenomic protocols are currently in use in clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implying the need for standardization of metagenomic analysis for use in clinical settings.
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Affiliation(s)
- F Xavier Lopez-Labrador
- Virology Laboratory, Genomics and Health Area, Center for Public Health Research (FISABIO-Public Health), Generalitat Valenciana, Valencia, Spain; Microbiology & Ecology Department, Medical School, University of Valencia, Spain; and CIBERESP, Instituto de Salud Carlos III, Spain
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Igor A Sidorov
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Julianne R Brown
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Lize Cuypers
- Department of Laboratory Medicine, University Hospitals Leuven, and Laboratory of Clinical Microbiology, KU, Leuven, Belgium
| | - Lies Laenen
- Department of Laboratory Medicine, University Hospitals Leuven, and Laboratory of Clinical Microbiology, KU, Leuven, Belgium
| | - Bert Vanmechelen
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Piet Maes
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Nicole Fischer
- University Medical Center Hamburg-Eppendorf, UKE Institute for Medical Microbiology, Virology and Hygiene, Germany
| | - Ian Pichler
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Nathaniel Storey
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Laura Atkinson
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Switzerland
| | | | | | | | | | | | - Ondrej Cinek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, and University Hospital Motol, Prague, Czech Republic
| | - Klára Hubáčková
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, and University Hospital Motol, Prague, Czech Republic
| | - Kees Mourik
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Stefan A Boers
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Lea Stauber
- Institute for Infectious Diseases, University of Bern, Switzerland
| | - Maud Salmona
- Virology Department, AP-HP, Hôpital Saint Louis, F-75010 Paris, France
| | | | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Switzerland
| | - Alessandra Franze'
- Virology Laboratory, Genomics and Health Area, Center for Public Health Research (FISABIO-Public Health), Generalitat Valenciana, Valencia, Spain
| | - Jerome LeGoff
- Virology Department, AP-HP, Hôpital Saint Louis, F-75010 Paris, France
| | - Eric C J Claas
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Jutte J C de Vries
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
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2
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Urban L, Perlas A, Francino O, Martí‐Carreras J, Muga BA, Mwangi JW, Boykin Okalebo L, Stanton JL, Black A, Waipara N, Fontsere C, Eccles D, Urel H, Reska T, Morales HE, Palmada‐Flores M, Marques‐Bonet T, Watsa M, Libke Z, Erkenswick G, van Oosterhout C. Real-time genomics for One Health. Mol Syst Biol 2023; 19:e11686. [PMID: 37325891 PMCID: PMC10407731 DOI: 10.15252/msb.202311686] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
The ongoing degradation of natural systems and other environmental changes has put our society at a crossroad with respect to our future relationship with our planet. While the concept of One Health describes how human health is inextricably linked with environmental health, many of these complex interdependencies are still not well-understood. Here, we describe how the advent of real-time genomic analyses can benefit One Health and how it can enable timely, in-depth ecosystem health assessments. We introduce nanopore sequencing as the only disruptive technology that currently allows for real-time genomic analyses and that is already being used worldwide to improve the accessibility and versatility of genomic sequencing. We showcase real-time genomic studies on zoonotic disease, food security, environmental microbiome, emerging pathogens, and their antimicrobial resistances, and on environmental health itself - from genomic resource creation for wildlife conservation to the monitoring of biodiversity, invasive species, and wildlife trafficking. We stress why equitable access to real-time genomics in the context of One Health will be paramount and discuss related practical, legal, and ethical limitations.
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Affiliation(s)
- Lara Urban
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- School of Life Sciences, Technical University of MunichFreisingGermany
| | - Albert Perlas
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
| | - Olga Francino
- Nano1Health SL, Parc de Recerca UABCampus Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Joan Martí‐Carreras
- Nano1Health SL, Parc de Recerca UABCampus Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Brenda A Muga
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
| | | | | | | | - Amanda Black
- Bioprotection AotearoaLincoln UniversityLincolnNew Zealand
| | | | - Claudia Fontsere
- Center for Evolutionary HologenomicsThe Globe Institute, University of CopenhagenCopenhagenDenmark
| | - David Eccles
- Hugh Green Cytometry CentreMalaghan Institute of Medical ResearchWellingtonNew Zealand
| | - Harika Urel
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- School of Life Sciences, Technical University of MunichFreisingGermany
| | - Tim Reska
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- School of Life Sciences, Technical University of MunichFreisingGermany
| | - Hernán E Morales
- Center for Evolutionary HologenomicsThe Globe Institute, University of CopenhagenCopenhagenDenmark
- Department of Biology, Ecology BuildingLund UniversityLundSweden
| | - Marc Palmada‐Flores
- Institute of Evolutionary BiologyUniversitat Pompeu Fabra‐CSIC, PRBBBarcelonaSpain
| | - Tomas Marques‐Bonet
- Institute of Evolutionary BiologyUniversitat Pompeu Fabra‐CSIC, PRBBBarcelonaSpain
- Catalan Institution of Research and Advanced Studies (ICREA)BarcelonaSpain
- CNAGCentre of Genomic AnalysisBarcelonaSpain
- Institut Català de Paleontologia Miquel CrusafontUniversitat Autònoma de BarcelonaBarcelonaSpain
| | | | - Zane Libke
- Instituto Nacional de BiodiversidadQuitoEcuador
- Fundación Sumak Kawsay In SituCantón MeraEcuador
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3
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Ring N, Low AS, Wee B, Paterson GK, Nuttall T, Gally D, Mellanby R, Fitzgerald JR. Rapid metagenomic sequencing for diagnosis and antimicrobial sensitivity prediction of canine bacterial infections. Microb Genom 2023; 9:mgen001066. [PMID: 37471128 PMCID: PMC10438823 DOI: 10.1099/mgen.0.001066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/18/2023] [Indexed: 07/21/2023] Open
Abstract
Antimicrobial resistance is a major threat to human and animal health. There is an urgent need to ensure that antimicrobials are used appropriately to limit the emergence and impact of resistance. In the human and veterinary healthcare setting, traditional culture and antimicrobial sensitivity testing typically requires 48-72 h to identify appropriate antibiotics for treatment. In the meantime, broad-spectrum antimicrobials are often used, which may be ineffective or impact non-target commensal bacteria. Here, we present a rapid, culture-free, diagnostics pipeline, involving metagenomic nanopore sequencing directly from clinical urine and skin samples of dogs. We have planned this pipeline to be versatile and easily implementable in a clinical setting, with the potential for future adaptation to different sample types and animals. Using our approach, we can identify the bacterial pathogen present within 5 h, in some cases detecting species which are difficult to culture. For urine samples, we can predict antibiotic sensitivity with up to 95 % accuracy. Skin swabs usually have lower bacterial abundance and higher host DNA, confounding antibiotic sensitivity prediction; an additional host depletion step will likely be required during the processing of these, and other types of samples with high levels of host cell contamination. In summary, our pipeline represents an important step towards the design of individually tailored veterinary treatment plans on the same day as presentation, facilitating the effective use of antibiotics and promoting better antimicrobial stewardship.
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Affiliation(s)
- Natalie Ring
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Alison S. Low
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Bryan Wee
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Gavin K. Paterson
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Tim Nuttall
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - David Gally
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Richard Mellanby
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
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4
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Retrospective Detection and Complete Genomic Sequencing of Canine morbillivirus in Eurasian Otter (Lutra lutra) Using Nanopore Technology. Viruses 2022; 14:v14071433. [PMID: 35891411 PMCID: PMC9323228 DOI: 10.3390/v14071433] [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: 04/19/2022] [Revised: 06/16/2022] [Accepted: 06/28/2022] [Indexed: 12/02/2022] Open
Abstract
The Eurasian otter (Lutra lutra) is a piscivorous apex predator in aquatic habitats, and a flagship species of conservation biology throughout Europe. Despite the wide distribution and ecological relevance of the species, there is a considerable lack of knowledge regarding its virological and veterinary health context, especially in Central Europe. Canine morbillivirus (Canine distemper virus (CDV)) is a highly contagious viral agent of the family Paramyxoviridae with high epizootic potential and veterinary health impact. CDV is present worldwide among a wide range of animals; wild carnivores are at particular risk. As part of a retrospective study, lung-tissue samples (n = 339) from Eurasian otters were collected between 2000 and 2021 throughout Hungary. The samples were screened for CDV using a real-time RT-PCR method. Two specimens proved positive for CDV RNA. In one sample, the complete viral genome was sequenced using a novel, pan-genotype CDV-specific amplicon-based sequencing method with Oxford Nanopore sequencing technology. Both viral sequences were grouped to a European lineage based on the hemagglutinin-gene phylogenetic classification. In this article, we present the feasibility of road-killed animal samples for understanding the long-term dynamics of CDV among wildlife and provide novel virological sequence data to better understand CDV circulation and evolution.
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5
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Han S, Dadone L, Ferguson S, Bapodra-Villaverde P, Dennis PM, Aruho R, Sadar MJ, Fennessy J, Driciru M, Muneza AB, Brown MB, Johnston M, Lahmers K. Giraffe skin disease: Clinicopathologic characterization of cutaneous filariasis in the critically endangered Nubian giraffe ( Giraffa camelopardalis camelopardalis). Vet Pathol 2022; 59:467-475. [DOI: 10.1177/03009858221082606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Giraffe skin disease (GSD) is an emerging disease of free-ranging giraffe recognized in the last 25 years in several species, including the critically endangered Nubian giraffe ( Giraffa camelopardalis camelopardalis) of Uganda. Identifying the cause of GSD and understanding its impact on health were deemed paramount to supporting these vulnerable populations. Sixty-four giraffes were immobilized in Murchison Falls National Park, Uganda, from 2017 to 2019, and GSD lesions were opportunistically biopsied. Fifty-five giraffes (86%) had GSD lesions on the neck, axilla, chest, and cranial trunk. Lesions were categorized into early, intermediary, and dormant stages based on gross and histological characteristics. Early lesions were smaller, crusted nodules with eosinophilic and pyogranulomatous dermatitis and furunculosis. Intermediary lesions were thick plaques of proliferative and fissured hyperkeratosis and acanthosis with dense dermal granulation tissue and severe eosinophilic and granulomatous dermatitis. Lesions appeared to resolve to dormancy, with dormant lesions consisting of hairless plaques of hyperkeratosis with dermal scarring and residual inflammation. The periphery of early and intermediary lesions included follicular granulomas containing adult filarid nematodes, with myriad encysted microfilariae in the superficial dermis. Stage L3 larvae were common in early and intermediary lesions, and dormant lesions had remnant encysted microfilariae with no adult or stage L3 larvae. Nematodes were morphologically and genetically novel with close identity to Stephanofilaria spp. and Brugia malayi, which cause infectious filariasis. Identification of potential insect vectors, long-term monitoring of GSD lesions, and evaluating response to therapy is ongoing in the efforts to help conserve the Nubian giraffe.
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Affiliation(s)
- Sushan Han
- Colorado State University, Fort Collins, CO
| | | | | | | | | | | | | | | | | | | | - Michael B. Brown
- Giraffe Conservation Foundation, Windhoek, Namibia
- Smithsonian’s National Zoo & Conservation Biology Institute, Front Royal, VA
- Dartmouth College, Hanover, NH
| | | | - Kevin Lahmers
- Virginia Tech Animal Laboratory Services, Blacksburg, VA
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6
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Lanszki Z, Tóth GE, Schütz É, Zeghbib S, Rusvai M, Jakab F, Kemenesi G. Complete genomic sequencing of canine distemper virus with nanopore technology during an epizootic event. Sci Rep 2022; 12:4116. [PMID: 35260784 PMCID: PMC8904823 DOI: 10.1038/s41598-022-08183-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/03/2022] [Indexed: 02/05/2023] Open
Abstract
Canine distemper virus (CDV) endangers a wide range of wild animal populations, can cross species barriers and therefore representing a significant conservational and animal health risk around the globe. During spring to autumn 2021, according to our current estimates a minimum of 50 red foxes (Vulpes vulpes) died of CDV in Hungary, with CDV lesions. Oral, nasal and rectal swab samples were RT-PCR screened for Canine Distemper Virus from red fox carcasses. To investigate in more detail the origins of these CDV strains, 19 complete genomes were sequenced with a pan-genotype CDV-specific amplicon-based sequencing method developed by our laboratory and optimized for the Oxford Nanopore Technologies platform. Phylogenetic analysis of the complete genomic sequences and separately the hemagglutinin gene sequences revealed the role of the Europe lineage of CDV as a causative agent for the current epizootic. Here we highlight the growing importance of fast developing rapid sequencing technologies to aid rapid response activities during epidemics or epizootic events. We also emphasize the urgent need for improved surveillance of CDV, considering the epizootic capability of enzootic strains as reported in the current study. For such future efforts, we provide a novel NGS protocol to facilitate future genomic surveillance studies.
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Affiliation(s)
- Zsófia Lanszki
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, 7624, Hungary.,Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, 7624, Hungary
| | - Gábor E Tóth
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, 7624, Hungary.,Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, 7624, Hungary
| | - Éva Schütz
- Exo-Pet Állatgyógyászati Centrum, Budapest, 1078, Hungary
| | - Safia Zeghbib
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, 7624, Hungary.,Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, 7624, Hungary
| | | | - Ferenc Jakab
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, 7624, Hungary.,Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, 7624, Hungary
| | - Gábor Kemenesi
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, 7624, Hungary. .,Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, 7624, Hungary.
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7
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Brancaccio RN, Robitaille A, Dutta S, Rollison DE, Tommasino M, Gheit T. MinION nanopore sequencing and assembly of a complete human papillomavirus genome. J Virol Methods 2021; 294:114180. [PMID: 33965458 PMCID: PMC8223502 DOI: 10.1016/j.jviromet.2021.114180] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/26/2021] [Accepted: 05/03/2021] [Indexed: 01/01/2023]
Abstract
BACKGROUND The MinION sequencer belongs to the third generation of sequencing technology that allows for the generation of ultra-long reads, representing a potentially more effective approach to characterize entire viral genome sequences than other time-consuming and low-throughput methodologies. METHODS We report the use of the MinION nanopore sequencer to sequence the full-length genome of human papillomavirus (HPV)-ICB2 (7441 bp), which was previously characterized in our laboratory. Three independent MinION libraries were prepared and sequenced using either three consecutive 12 -h runs (Protocol A) or a single run of 48 h starting from a pool of three barcoded DNA libraries (Protocol B). A fully automated bioinformatics pipeline was developed for the reconstruction of the viral genome. RESULTS Protocols A and B generated 9,354,933 and 3,255,879 reads, respectively. Read length N50 values ranged between 6976 and 7360 nucleotides over the four sequencing runs. Bioinformatics analysis showed that both protocols allowed for the reconstruction of the whole viral genome, with pairwise percentages of identity to HPV-ICB2 of 100 % for protocol A and 99.98 % for protocol B. CONCLUSION Our results show that the use of the MinION nanopore sequencer represents an effective strategy for whole-genome sequencing of HPVs with a minimal error rate.
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Affiliation(s)
- Rosario N Brancaccio
- Early Detection, Prevention and Infections Branch, International Agency for Research on Cancer, Lyon, France
| | - Alexis Robitaille
- Early Detection, Prevention and Infections Branch, International Agency for Research on Cancer, Lyon, France
| | - Sankhadeep Dutta
- Chittaranjan National Cancer Institute, Department of Viral Associated Human Cancer, Kolkata, India
| | - Dana E Rollison
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Massimo Tommasino
- Early Detection, Prevention and Infections Branch, International Agency for Research on Cancer, Lyon, France
| | - Tarik Gheit
- Early Detection, Prevention and Infections Branch, International Agency for Research on Cancer, Lyon, France.
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8
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Zhu X, Yan S, Yuan F, Wan S. The Applications of Nanopore Sequencing Technology in Pathogenic Microorganism Detection. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2020; 2020:6675206. [PMID: 33488885 PMCID: PMC7790562 DOI: 10.1155/2020/6675206] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/04/2020] [Accepted: 12/18/2020] [Indexed: 12/23/2022]
Abstract
Infectious diseases are major threats to human health and lead to a serious public health burden. The emergence of new pathogens and the mutation of known pathogens challenge our ability to diagnose and control infectious diseases. Nanopore sequencing technology exhibited versatile applications in pathogenic microorganism detection due to its flexible data throughput. This review article introduced the applications of nanopore sequencing in clinical microbiology and infectious diseases management, including the monitoring of emerging infectious diseases outbreak, identification of pathogen drug resistance, and disease-related microbial communities characterization.
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Affiliation(s)
- Xiaojian Zhu
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou 341000, China
| | - Shanshan Yan
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, China
- Department of Publication Health and Health Management, Gannan Medical University, Ganzhou 341000, China
| | - Fenghua Yuan
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou 341000, China
| | - Shaogui Wan
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou 341000, China
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9
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Kiselev D, Matsvay A, Abramov I, Dedkov V, Shipulin G, Khafizov K. Current Trends in Diagnostics of Viral Infections of Unknown Etiology. Viruses 2020; 12:E211. [PMID: 32074965 PMCID: PMC7077230 DOI: 10.3390/v12020211] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 12/27/2022] Open
Abstract
Viruses are evolving at an alarming rate, spreading and inconspicuously adapting to cutting-edge therapies. Therefore, the search for rapid, informative and reliable diagnostic methods is becoming urgent as ever. Conventional clinical tests (PCR, serology, etc.) are being continually optimized, yet provide very limited data. Could high throughput sequencing (HTS) become the future gold standard in molecular diagnostics of viral infections? Compared to conventional clinical tests, HTS is universal and more precise at profiling pathogens. Nevertheless, it has not yet been widely accepted as a diagnostic tool, owing primarily to its high cost and the complexity of sample preparation and data analysis. Those obstacles must be tackled to integrate HTS into daily clinical practice. For this, three objectives are to be achieved: (1) designing and assessing universal protocols for library preparation, (2) assembling purpose-specific pipelines, and (3) building computational infrastructure to suit the needs and financial abilities of modern healthcare centers. Data harvested with HTS could not only augment diagnostics and help to choose the correct therapy, but also facilitate research in epidemiology, genetics and virology. This information, in turn, could significantly aid clinicians in battling viral infections.
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Affiliation(s)
- Daniel Kiselev
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- I.M. Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - Alina Matsvay
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- Moscow Institute of Physics and Technology, National Research University, 117303 Moscow, Russia
| | - Ivan Abramov
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
| | - Vladimir Dedkov
- Pasteur Institute, Federal Service on Consumers’ Rights Protection and Human Well-Being Surveillance, 197101 Saint-Petersburg, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - German Shipulin
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
| | - Kamil Khafizov
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- Moscow Institute of Physics and Technology, National Research University, 117303 Moscow, Russia
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10
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Ji P, Aw TG, Van Bonn W, Rose JB. Evaluation of a portable nanopore-based sequencer for detection of viruses in water. J Virol Methods 2019; 278:113805. [PMID: 31891731 DOI: 10.1016/j.jviromet.2019.113805] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 12/20/2022]
Abstract
The newly emerged nanopore sequencing technology such as MinION™ allows for real-time detection of long DNA/RNA fragments on a portable device, yet few have examined its performance for environmental viromes. Here we seeded one RNA virus bacteriophage MS2 and one DNA virus bacteriophage PhiX174 into 10 L well water at three levels ranging from 1 to 21,100 plaque-forming units (PFU)/mL. Two workflows were established to maximize the number of sequencing reads of RNA and DNA viruses using MinION™. With dead-end ultrafiltration, PEG precipitation, and random amplification, MinION™ was capable of detecting MS2 at 155 PFU/mL and PhiX174 at 1-2 PFU/mL. While the DNA workflow only detected PhiX174, the RNA workflow detected both MS2 and PhiX174. The virus concentration, or relative abundance of viral nucleic acids in total nucleic acids, is critical to the proportion of viral reads in sequencing results. Our findings also highlight the importance of including control samples in sequencing runs for environmental water samples with low virus abundance.
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Affiliation(s)
- Pan Ji
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
| | - Tiong Gim Aw
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - William Van Bonn
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA; A. Watson Armour III Center for Animal Health and Welfare, John G. Shedd Aquarium, Chicago, IL 60605, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA.
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11
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Diagnosis and characterization of canine distemper virus through sequencing by MinION nanopore technology. Sci Rep 2019; 9:1714. [PMID: 30737428 PMCID: PMC6368598 DOI: 10.1038/s41598-018-37497-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 12/06/2018] [Indexed: 11/08/2022] Open
Abstract
Prompt identification of the causative pathogen of an infectious disease is essential for the choice of treatment or preventive measures. In this perspective, nucleic acids purified from the brain tissue of a dog succumbed after severe neurological signs were processed with the MinION (Oxford Nanopore Technologies, Oxford UK) sequencing technology. Canine distemper virus (CDV) sequence reads were detected. Subsequently, a specific molecular test and immunohistochemistry were used to confirm the presence of CDV RNA and antigen, respectively, in tissues. This study supports the use of the NGS in veterinary clinical practice with potential advantages in terms of rapidity and broad-range of molecular diagnosis.
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12
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Ramsauer AS, Kubacki J, Welle M, Bachofen C, Fraefel C, Hoby S, Tobler K, Wenker C. Detection and Characterization of Okapi (Okapia johnstoni)-specific Papillomavirus type 1 (OjPV1). Vet Microbiol 2018; 223:113-118. [PMID: 30173736 DOI: 10.1016/j.vetmic.2018.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/25/2018] [Accepted: 08/05/2018] [Indexed: 11/27/2022]
Abstract
Papillomavirus-specific DNA was detected in skin lesions collected from an okapi (Okapia johnstoni) in the Zoo Basel. According to the nucleotide sequence analysis, the virus belongs to the genus Deltapapillomavirus. Based on bioinformatics analysis, we propose to designate the newly identified virus as Okapia johnstoni Papillomavirus type 1 (OjPV1). OjPV1 is genetically most closely related to a recently described giraffe (Giraffa camelopardalis) -specific papillomavirus (GcPV1). Of note, the putative oncogenic E5 proteins from OjPV1 and GcPV1 are more conserved than the L1 proteins. This indicates, that the selection pressure on E5 may be more pronounced than that on the otherwise most conserved major capsid protein L1.
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Affiliation(s)
- Anna Sophie Ramsauer
- Virologisches Institut, Vetsuisse Fakultät, Universität Zürich, Winterthurerstrasse 266a, CH-8057, Zürich, Switzerland.
| | - Jakub Kubacki
- Virologisches Institut, Vetsuisse Fakultät, Universität Zürich, Winterthurerstrasse 266a, CH-8057, Zürich, Switzerland
| | - Monika Welle
- Institut für Tierpathologie, Dermfocus, Vetsuisse Fakultät, Universität Bern, Postfach, CH-3001, Bern, Switzerland
| | - Claudia Bachofen
- Virologisches Institut, Vetsuisse Fakultät, Universität Zürich, Winterthurerstrasse 266a, CH-8057, Zürich, Switzerland
| | - Cornel Fraefel
- Virologisches Institut, Vetsuisse Fakultät, Universität Zürich, Winterthurerstrasse 266a, CH-8057, Zürich, Switzerland
| | - Stefan Hoby
- Zoo Basel, Binningerstrasse 40, CH-4054, Basel, Switzerland
| | - Kurt Tobler
- Virologisches Institut, Vetsuisse Fakultät, Universität Zürich, Winterthurerstrasse 266a, CH-8057, Zürich, Switzerland
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13
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Theuns S, Vanmechelen B, Bernaert Q, Deboutte W, Vandenhole M, Beller L, Matthijnssens J, Maes P, Nauwynck HJ. Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus. Sci Rep 2018; 8:9830. [PMID: 29959349 PMCID: PMC6026206 DOI: 10.1038/s41598-018-28180-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/18/2018] [Indexed: 11/13/2022] Open
Abstract
Enteric diseases in swine are often caused by different pathogens and thus metagenomics are a useful tool for diagnostics. The capacities of nanopore sequencing for viral diagnostics were investigated here. First, cell culture-grown porcine epidemic diarrhea virus and rotavirus A were pooled and sequenced on a MinION. Reads were already detected at 7 seconds after start of sequencing, resulting in high sequencing depths (19.2 to 103.5X) after 3 h. Next, diarrheic feces of a one-week-old piglet was analyzed. Almost all reads (99%) belonged to bacteriophages, which may have reshaped the piglet's microbiome. Contigs matched Bacteroides, Escherichia and Enterococcus phages. Moreover, porcine kobuvirus was discovered in the feces for the first time in Belgium. Suckling piglets shed kobuvirus from one week of age, but an association between peak of viral shedding (106.42-107.01 copies/swab) and diarrheic signs was not observed during a follow-up study. Retrospective analysis showed the widespread (n = 25, 56.8% positive) of genetically moderately related kobuviruses among Belgian diarrheic piglets. MinION enables rapid detection of enteric viruses. Such new methodologies will change diagnostics, but more extensive validations should be conducted. The true enteric pathogenicity of porcine kobuvirus should be questioned, while its subclinical importance cannot be excluded.
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Affiliation(s)
- Sebastiaan Theuns
- Ghent University, Faculty of Veterinary Medicine, Department of Virology, Parasitology and Immunology, Laboratory of Virology, Merelbeke, Belgium.
| | - Bert Vanmechelen
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, Leuven, Belgium
| | - Quinten Bernaert
- Ghent University, Faculty of Veterinary Medicine, Department of Virology, Parasitology and Immunology, Laboratory of Virology, Merelbeke, Belgium
| | - Ward Deboutte
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Viral Metagenomics, Rega Institute for Medical Research, Leuven, Belgium
| | - Marilou Vandenhole
- Ghent University, Faculty of Veterinary Medicine, Department of Virology, Parasitology and Immunology, Laboratory of Virology, Merelbeke, Belgium
| | - Leen Beller
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Viral Metagenomics, Rega Institute for Medical Research, Leuven, Belgium
| | - Jelle Matthijnssens
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Viral Metagenomics, Rega Institute for Medical Research, Leuven, Belgium
| | - Piet Maes
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, Leuven, Belgium
| | - Hans J Nauwynck
- Ghent University, Faculty of Veterinary Medicine, Department of Virology, Parasitology and Immunology, Laboratory of Virology, Merelbeke, Belgium
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