{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T08:18:46Z","timestamp":1790756326093,"version":"4.1.0"},"reference-count":36,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2019,8,29]],"date-time":"2019-08-29T00:00:00Z","timestamp":1567036800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006447","name":"Universit\u00e4t Z\u00fcrich","doi-asserted-by":"publisher","award":["Clinical Research Priority Program"],"award-info":[{"award-number":["Clinical Research Priority Program"]}],"id":[{"id":"10.13039\/501100006447","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Metagenomic next-generation sequencing (mNGS) can capture the full spectrum of viral pathogens in a specimen and has the potential to become an all-in-one solution for virus diagnostics. To date, clinical application is still in an early phase and limitations remain. Here, we evaluated the impact of viral mNGS for cases analyzed over two years in a tertiary diagnostics unit. High throughput mNGS was performed upon request by the treating clinician in cases where the etiology of infection remained unknown or the initial differential diagnosis was very broad. The results were compared to conventional routine testing regarding outcome and workload. In total, 163 specimens from 105 patients were sequenced. The main sample types were cerebrospinal fluid (34%), blood (33%) and throat swabs (10%). In the majority of the cases, viral encephalitis\/meningitis or respiratory infection was suspected. In parallel, conventional virus diagnostic tests were performed (mean 18.5 individually probed targets\/patients). mNGS detected viruses in 34 cases (32%). While often confirmatory, in multiple cases, the identified viruses were not included in the selected routine diagnostic tests. Two years of mNGS in a tertiary diagnostics unit demonstrated the advantages of a single, untargeted approach for comprehensive, rapid and efficient virus diagnostics, confirming the utility of mNGS in complementing current routine tests.<\/jats:p>","DOI":"10.3390\/genes10090661","type":"journal-article","created":{"date-parts":[[2019,8,29]],"date-time":"2019-08-29T11:26:22Z","timestamp":1567077982000},"page":"661","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":61,"title":["Two Years of Viral Metagenomics in a Tertiary Diagnostics Unit: Evaluation of the First 105 Cases"],"prefix":"10.3390","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4233-5952","authenticated-orcid":false,"given":"Verena","family":"Kufner","sequence":"first","affiliation":[{"name":"Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Plate","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1955-7007","authenticated-orcid":false,"given":"Stefan","family":"Schmutz","sequence":"additional","affiliation":[{"name":"Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dominique L.","family":"Braun","sequence":"additional","affiliation":[{"name":"Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland"},{"name":"Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1142-6723","authenticated-orcid":false,"given":"Huldrych F.","family":"G\u00fcnthard","sequence":"additional","affiliation":[{"name":"Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland"},{"name":"Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Riccarda","family":"Capaul","sequence":"additional","affiliation":[{"name":"Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Zbinden","sequence":"additional","affiliation":[{"name":"Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1059-3191","authenticated-orcid":false,"given":"Nicolas J.","family":"Mueller","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra","family":"Trkola","sequence":"additional","affiliation":[{"name":"Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0384-0000","authenticated-orcid":false,"given":"Michael","family":"Huber","sequence":"additional","affiliation":[{"name":"Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2019,8,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1565","DOI":"10.1086\/509330","article-title":"Beyond viruses: clinical profiles and etiologies associated with encephalitis","volume":"43","author":"Glaser","year":"2006","journal-title":"Clin. Infect. Dis."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1254","DOI":"10.1183\/09031936.02.01942001","article-title":"Factors associated with unknown aetiology in patients with community-acquired pneumonia","volume":"20","author":"Ewig","year":"2002","journal-title":"Eur. Respir. J."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1097\/MD.0b013e31802fe858","article-title":"A prospective multicenter study on fever of unknown origin: The yield of a structured diagnostic protocol","volume":"86","author":"Vos","year":"2007","journal-title":"Medicine (Baltimore)"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"2382","DOI":"10.1056\/NEJMoa1500245","article-title":"Community-acquired pneumonia requiring hospitalization","volume":"373","author":"Jain","year":"2015","journal-title":"N. Engl. J. Med."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1080\/14737159.2018.1487292","article-title":"The challenge of diagnostic metagenomics","volume":"18","author":"Greninger","year":"2018","journal-title":"Expert Rev. Mol. Diagn."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1002\/rmv.532","article-title":"Viral metagenomics","volume":"17","author":"Delwart","year":"2007","journal-title":"Rev. Med. Virol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"ofx121","DOI":"10.1093\/ofid\/ofx121","article-title":"Hepatitis E virus-associated meningoencephalitis in a lung transplant recipient diagnosed by clinical metagenomic sequencing","volume":"4","author":"Murkey","year":"2017","journal-title":"Open Forum Infect. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1002\/ana.24982","article-title":"A novel cause of chronic viral meningoencephalitis: Cache Valley virus","volume":"82","author":"Wilson","year":"2017","journal-title":"Ann. Neurol."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Pastrana, D.V., Peretti, A., Welch, N.L., Borgogna, C., Olivero, C., Badolato, R., Notarangelo, L.D., Gariglio, M., FitzGerald, P.C., and McIntosh, C.E. (2018). Metagenomic discovery of 83 new human papillomavirus types in patients with immunodeficiency. mSphere, 3.","DOI":"10.1128\/mSphereDirect.00645-18"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"2360","DOI":"10.1038\/s41598-019-38975-z","article-title":"Viral metagenomics revealed novel betatorquevirus species in pediatric inpatients with encephalitis\/meningoencephalitis from Ghana","volume":"9","author":"Eibach","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1056\/NEJMoa1203378","article-title":"A new phlebovirus associated with severe febrile illness in Missouri","volume":"367","author":"McMullan","year":"2012","journal-title":"N. Engl. J. Med."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1016\/j.jinf.2017.12.014","article-title":"Encephalitis diagnosis using metagenomics: application of next generation sequencing for undiagnosed cases","volume":"76","author":"Brown","year":"2018","journal-title":"J. Infect."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.jbiotec.2016.12.022","article-title":"Application of next generation sequencing in clinical microbiology and infection prevention","volume":"243","author":"Deurenberg","year":"2017","journal-title":"J. Biotechnol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1146\/annurev-pathmechdis-012418-012751","article-title":"Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection","volume":"14","author":"Gu","year":"2019","journal-title":"Annu. Rev. Pathol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"2327","DOI":"10.1056\/NEJMoa1803396","article-title":"Clinical metagenomic sequencing for diagnosis of meningitis and encephalitis","volume":"380","author":"Wilson","year":"2019","journal-title":"N. Engl. J. Med."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1016\/j.cmi.2018.12.022","article-title":"High-throughput sequencing for the aetiologic identification of viral encephalitis, meningoencephalitis, and meningitis. A narrative review and clinical appraisal","volume":"25","author":"Zanella","year":"2019","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Rupp\u00e9, E., and Schrenzel, J. (2019). Messages from the third International Conference on Clinical Metagenomics (ICCMg3). Microbes Infect., 1\u201318.","DOI":"10.1016\/j.micinf.2019.02.004"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"4642","DOI":"10.1128\/JVI.02301-08","article-title":"Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis","volume":"83","author":"Victoria","year":"2009","journal-title":"J. Virol."},{"key":"ref_19","first-page":"1","article-title":"Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis","volume":"13","author":"Greninger","year":"2015","journal-title":"Genome Med."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"e01491-15","DOI":"10.1128\/mBio.01491-15","article-title":"Virome capture sequencing enables sensitive viral diagnosis and comprehensive virome analysis","volume":"6","author":"Briese","year":"2015","journal-title":"mBio"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1101\/gr.238170.118","article-title":"Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid","volume":"29","author":"Miller","year":"2019","journal-title":"Genome Res."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Luk, K.-C., Berg, M.G., Naccache, S.N., Kabre, B., Federman, S., Mbanya, D., Kaptu\u00e9, L., Chiu, C.Y., Brennan, C.A., and Hackett, J. (2015). Utility of metagenomic next-generation sequencing for characterization of HIV and human Pegivirus diversity. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0141723"},{"key":"ref_23","first-page":"2095","article-title":"Understanding the promises and hurdles of metagenomic next-generation sequencing as a diagnostic tool for infectious diseases","volume":"380","author":"Simner","year":"2017","journal-title":"Clin. Infect. Dis"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1007\/s10096-019-03520-3","article-title":"Understanding and overcoming the pitfalls and biases of next-generation sequencing (NGS) methods for use in the routine clinical microbiological diagnostic laboratory","volume":"38","author":"Boers","year":"2019","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1038\/nrg.2017.44","article-title":"Reference standards for next-generation sequencing","volume":"18","author":"Hardwick","year":"2017","journal-title":"Nat. Rev. Genet."},{"key":"ref_26","first-page":"1","article-title":"Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples","volume":"5","author":"Lewandowska","year":"2017","journal-title":"Microbiome"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.diagmicrobio.2015.06.017","article-title":"Unbiased metagenomic sequencing complements specific routine diagnostic methods and increases chances to detect rare viral strains","volume":"83","author":"Lewandowska","year":"2015","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12879-018-2946-7","article-title":"Persistent mammalian orthoreovirus, coxsackievirus and adenovirus co-infection in a child with a primary immunodeficiency detected by metagenomic sequencing: A case report","volume":"18","author":"Lewandowska","year":"2018","journal-title":"BMC Infect. Dis."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12879-019-4231-9","article-title":"Meningitis and epididymitis caused by Toscana virus infection imported to Switzerland diagnosed by metagenomic sequencing: A case report","volume":"19","author":"Tschumi","year":"2019","journal-title":"BMC Infect. Dis."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"e1006292","DOI":"10.1371\/journal.ppat.1006292","article-title":"The blood DNA virome in 8,000 humans","volume":"13","author":"Moustafa","year":"2017","journal-title":"PLoS Pathog."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Ondov, B.D., Bergman, N.H., and Phillippy, A.M. (2011). Interactive metagenomic visualization in a Web browser. BMC Bioinform., 12.","DOI":"10.1186\/1471-2105-12-385"},{"key":"ref_32","unstructured":"Kaiser, L. (2019, July 31). Virome and Transplantation. Available online: https:\/\/www.eccmidlive.org\/#resources\/virome-and-transplantation."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/s40168-018-0507-3","article-title":"Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses","volume":"6","year":"2018","journal-title":"Microbiome"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T.L. (2009). BLAST+: Architecture and applications. BMC Bioinform., 10.","DOI":"10.1186\/1471-2105-10-421"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1785","DOI":"10.3201\/eid2410.180161","article-title":"Human Pegivirus in patients with encephalitis of unclear etiology, Poland","volume":"24","author":"Perlejewski","year":"2018","journal-title":"Emerg. Infect. Dis."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/10\/9\/661\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T13:15:10Z","timestamp":1760188510000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/10\/9\/661"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,8,29]]},"references-count":36,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2019,9]]}},"alternative-id":["genes10090661"],"URL":"https:\/\/doi.org\/10.3390\/genes10090661","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,8,29]]}}}