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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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de Frémont GM, Salmona M, Maillet F, Garzaro M, Bertinchamp R, Simonnet A, Feghoul L, Maki G, Roelens M, Chotard E, Picard C, Oksenhendler E, LeGoff J, Boutboul D. Human adenoviral (HAdV) chronic arthritis expands the infectious spectrum of primary agammaglobulinemia. Virol J 2022; 19:172. [PMID: 36316777 PMCID: PMC9623974 DOI: 10.1186/s12985-022-01905-z] [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: 09/09/2022] [Revised: 09/09/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022] Open
Abstract
Inborn errors of immunity (IEI) are a heterogeneous entity with an increasing number of late diagnoses. Besides infections, inflammatory manifestations are a growing part of the clinical landscape of IEI. These complications are of unknown causes and often lead to the prescription of immunosuppressive agents that worsen the underlying immune defect. We here report the case of an adult patient diagnosed with chronic Human Adenovirus C-1 arthritis in the setting of primary agammaglobulinemia. Metagenomic next-generation sequencing led to the correct diagnosis and high-dose intravenous immunoglobulins resulted in complete recovery. This observation gives new insights into adenoviral immunity and underlines the importance of metagenomics in the diagnosis of inflammatory manifestations in immunocompromised patients.
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Affiliation(s)
- Grégoire Martin de Frémont
- grid.413328.f0000 0001 2300 6614Clinical Immunology Department, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, Paris, France
| | - Maud Salmona
- grid.413328.f0000 0001 2300 6614Virology Department, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, Paris, France
| | - François Maillet
- grid.413328.f0000 0001 2300 6614Clinical Immunology Department, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, Paris, France
| | - Margaux Garzaro
- grid.413328.f0000 0001 2300 6614Clinical Immunology Department, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, Paris, France
| | - Rémi Bertinchamp
- grid.413328.f0000 0001 2300 6614Clinical Immunology Department, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, Paris, France
| | - Arthur Simonnet
- grid.413328.f0000 0001 2300 6614Clinical Immunology Department, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, Paris, France
| | - Linda Feghoul
- grid.413328.f0000 0001 2300 6614Virology Department, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, Paris, France
| | - Guitta Maki
- grid.413328.f0000 0001 2300 6614Immunology Laboratory, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, Paris, France
| | - Marie Roelens
- grid.412134.10000 0004 0593 9113Centre d’étude des déficits immunitaires (CEDI), Hôpital Necker, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, Paris, France
| | - Emilie Chotard
- grid.411296.90000 0000 9725 279XRheumatology Department, Hôpital Lariboisière, Assistance Publique-Hôpitaux de Paris (AP- HP), Université Paris Cité, Paris, France
| | - Capucine Picard
- grid.412134.10000 0004 0593 9113Centre d’étude des déficits immunitaires (CEDI), Hôpital Necker, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, Paris, France ,grid.462336.6INSERM U1163, Université Paris Cité, Imagine Institute, Paris, France
| | - Eric Oksenhendler
- grid.413328.f0000 0001 2300 6614Clinical Immunology Department, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, Paris, France
| | - Jérôme LeGoff
- grid.413328.f0000 0001 2300 6614Virology Department, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, Paris, France ,grid.462420.60000 0004 0638 4500Inserm U976, Université Paris Cité, Paris, France
| | - David Boutboul
- grid.413328.f0000 0001 2300 6614Clinical Immunology Department, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, Paris, France ,grid.462420.60000 0004 0638 4500Inserm U976, Université Paris Cité, Paris, France
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Prezioso C, Van Ghelue M, Moens U, Pietropaolo V. HPyV6 and HPyV7 in urine from immunocompromised patients. Virol J 2021; 18:24. [PMID: 33482864 PMCID: PMC7821732 DOI: 10.1186/s12985-021-01496-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/12/2021] [Indexed: 12/20/2022] Open
Abstract
Background Human polyomavirus 6 (HPyV6) and HPyV7 are two of the novel polyomaviruses that were originally detected in non-diseased skin. Serological studies have shown that these viruses are ubiquitous in the healthy adult population with seroprevalence up to 88% for HPyV6 and 72% for HPyV7. Both viruses are associated with pruritic skin eruption in immunocompromised patients, but a role with other diseases in immunoincompetent patients or malignancies has not been established. Methods PCR was used to determine the presence of HPyV6 and HPyV7 DNA in urine samples from systemic lupus erythematosus (n = 73), multiple sclerosis (n = 50), psoriasis vulgaris (n = 15), arthritic psoriasis (n = 15) and HIV-positive patients (n = 66). In addition, urine from pregnant women (n = 47) and healthy blood donors (n = 20) was investigated. Results HPyV6 DNA was detected in 21 (28.8%) of the urine specimens from SLE patients, in 6 (9.1%) of the urine samples from the HIV-positive cohort, and in 19 (40.4%) samples from pregnant women. HPyV7 DNA was only found in 6 (8.2%) of the urine specimens from SLE patients and in 4 (8.5%) samples from pregnant women. No HPyV6 and HPyV7 viruria was detected in the urine samples from the other patients. Conclusions HPyV6, and to a lesser extend HPyV7, viruria seems to be common in SLE and HIV-positive patients, and pregnant women. Whether these viruses are of clinical relevance in these patients is not known.
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Affiliation(s)
- Carla Prezioso
- Department of Public Health and Infectious Diseases, "Sapienza" University of Rome, Rome, Italy.,Microbiology of Chronic Neuro-Degenerative Pathologies, IRCSS San Raffaele Pisana, Rome, Italy
| | - Marijke Van Ghelue
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway.,Department of Clinical Medicine Faculty of Health Sciences, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Ugo Moens
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø - The Arctic University of Norway, Tromsø, Norway.
| | - Valeria Pietropaolo
- Department of Public Health and Infectious Diseases, "Sapienza" University of Rome, Rome, Italy.
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