{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T10:11:54Z","timestamp":1776852714705,"version":"3.51.2"},"reference-count":29,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2022,2,11]],"date-time":"2022-02-11T00:00:00Z","timestamp":1644537600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Introduction: Immunocompromised patients are prone to reactivations and (re-)infections of multiple DNA viruses. Viral load monitoring by single-target quantitative PCRs (qPCR) is the current cornerstone for virus quantification. In this study, a metagenomic next-generation sequencing (mNGS) approach was used for the identification and load monitoring of transplantation-related DNA viruses. Methods: Longitudinal plasma samples from six patients that were qPCR-positive for cytomegalovirus (CMV), Epstein-Barr virus (EBV), BK polyomavirus (BKV), adenovirus (ADV), parvovirus B19 (B19V), and torque teno-virus (TTV) were sequenced using the quantitative metagenomic Galileo Viral Panel Solution (Arc Bio, LLC, Cambridge, MA, USA) reagents and bioinformatics pipeline combination. Qualitative and quantitative performance was analysed with a focus on viral load ranges relevant for clinical decision making. Results: All pathogens identified by qPCR were also identified by mNGS. BKV, CMV, and HHV6B were additionally detected by mNGS, and could be confirmed by qPCR or auxiliary bioinformatic analysis. Viral loads determined by mNGS correlated with the qPCR results, with inter-method differences in viral load per virus ranging from 0.19 log10 IU\/mL for EBV to 0.90 log10 copies\/mL for ADV. TTV, analysed by mNGS in a semi-quantitative way, demonstrated a mean difference of 3.0 log10 copies\/mL. Trends over time in viral load determined by mNGS and qPCR were comparable, and clinical thresholds for initiation of treatment were equally identified by mNGS. Conclusions: The Galileo Viral Panel for quantitative mNGS performed comparably to qPCR concerning detection and viral load determination, within clinically relevant ranges of patient management algorithms.<\/jats:p>","DOI":"10.3390\/pathogens11020236","type":"journal-article","created":{"date-parts":[[2022,2,14]],"date-time":"2022-02-14T03:46:00Z","timestamp":1644810360000},"page":"236","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Longitudinal Monitoring of DNA Viral Loads in Transplant Patients Using Quantitative Metagenomic Next-Generation Sequencing"],"prefix":"10.3390","volume":"11","author":[{"given":"Ellen","family":"Carbo","sequence":"first","affiliation":[{"name":"Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anne","family":"Russcher","sequence":"additional","affiliation":[{"name":"Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1723-4570","authenticated-orcid":false,"given":"Margriet","family":"Kraakman","sequence":"additional","affiliation":[{"name":"Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9117-6658","authenticated-orcid":false,"given":"Caroline","family":"de Brouwer","sequence":"additional","affiliation":[{"name":"Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Igor","family":"Sidorov","sequence":"additional","affiliation":[{"name":"Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mariet","family":"Feltkamp","sequence":"additional","affiliation":[{"name":"Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9866-2461","authenticated-orcid":false,"given":"Aloys","family":"Kroes","sequence":"additional","affiliation":[{"name":"Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"Claas","sequence":"additional","affiliation":[{"name":"Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jutte","family":"de Vries","sequence":"additional","affiliation":[{"name":"Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,2,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1128\/CMR.13.1.83","article-title":"New Strategies for Prevention and Therapy of Cytomegalovirus Infection and Disease in Solid-Organ Transplant Recipients","volume":"13","author":"Sia","year":"2000","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"104566","DOI":"10.1016\/j.jcv.2020.104566","article-title":"Improved diagnosis of viral encephalitis in adult and pediatric hematological patients using viral metagenomics","volume":"130","author":"Carbo","year":"2020","journal-title":"J. Clin. Virol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"104940","DOI":"10.1016\/j.jcv.2021.104940","article-title":"Viral metagenomic sequencing in a cohort of international travellers returning with febrile illness","volume":"143","author":"Reyes","year":"2021","journal-title":"J. Clin. Virol."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Van Rijn, A.L., Van Boheemen, S., Sidorov, I., Carbo, E.C., Pappas, N., Mei, H., Feltkamp, M., Aanerud, M., Bakke, P., and Claas, E.C.J. (2019). The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease. PLoS ONE, 14.","DOI":"10.1101\/509919"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1016\/j.jmoldx.2019.10.007","article-title":"Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients","volume":"22","author":"Pappas","year":"2020","journal-title":"J. Mol. Diagn."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"104908","DOI":"10.1016\/j.jcv.2021.104908","article-title":"Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples","volume":"141","author":"Brown","year":"2021","journal-title":"J. Clin. Virol."},{"key":"ref_7","first-page":"104691","article-title":"Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure","volume":"134","author":"Brown","year":"2020","journal-title":"J. Clin. Virol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"104812","DOI":"10.1016\/j.jcv.2021.104812","article-title":"Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: Bioinformatic analysis and reporting","volume":"138","author":"Brown","year":"2021","journal-title":"J. Clin. Virol."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Cai, G., Li, H., Lu, Y., Huang, X., Lee, J., M\u00fcller, P., Ji, Y., and Liang, S. (2012). Accuracy of RNA-Seq and its dependence on sequencing depth. BMC Bioinform., 13.","DOI":"10.1186\/1471-2105-13-S13-S5"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1038\/nbt.2450","article-title":"Differential analysis of gene regulation at transcript resolution with RNA-seq","volume":"31","author":"Trapnell","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1101\/pdb.top084970","article-title":"RNA Sequencing and Analysis","volume":"2015","author":"Kukurba","year":"2015","journal-title":"Cold Spring Harb. Protoc."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1964","DOI":"10.3201\/eid2310.161986","article-title":"Diagnosis of Fatal Human Case of St. Louis Encephalitis Virus Infection by Metagenomic Sequencing, California, 2016","volume":"23","author":"Chiu","year":"2017","journal-title":"Emerg. Infect. Dis."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"e01113-19","DOI":"10.1128\/JCM.01113-19","article-title":"Metagenomic Next-Generation Sequencing for Identification and Quantitation of Transplant-Related DNA Viruses","volume":"57","author":"Carpenter","year":"2019","journal-title":"J. Clin. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1016\/j.jmoldx.2021.02.008","article-title":"Evaluation of a Next-Generation Sequencing Metagenomics Assay to Detect and Quantify DNA Viruses in Plasma from Transplant Recipients","volume":"23","author":"Sam","year":"2021","journal-title":"J. Mol. Diagn."},{"key":"ref_15","unstructured":"(2020, August 27). ArcBio Galileo Transplant WebApp. Available online: Galileo.arcbio.com."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1721","DOI":"10.1101\/gr.210641.116","article-title":"Centrifuge: Rapid and sensitive classification of metagenomic sequences","volume":"26","author":"Kim","year":"2016","journal-title":"Genome Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1093\/bioinformatics\/bty695","article-title":"Genome Detective: An automated system for virus identification from high-throughput sequencing data","volume":"35","author":"Vilsker","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"e13512","DOI":"10.1111\/ctr.13512","article-title":"Cytomegalovirus in solid organ transplant recipients\u2014Guidelines of the American Society of Transplantation Infectious Diseases Community of Practice","volume":"33","author":"Razonable","year":"2019","journal-title":"Clin. Transplant."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"e13528","DOI":"10.1111\/ctr.13528","article-title":"AST Infectious Diseases Community of Practice BK polyomavirus in solid organ transplantation\u2014Guidelines from the American Society of Transplantation Infectious Diseases Community of Practice","volume":"33","author":"Hirsch","year":"2019","journal-title":"Clin. Transplant."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"3571","DOI":"10.1002\/1873-3468.13576","article-title":"Adenovirus persistence, reactivation, and clinical management","volume":"593","author":"Lion","year":"2019","journal-title":"FEBS Lett."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Manaresi, E., and Gallinella, G. (2019). Advances in the Development of Antiviral Strategies against Parvovirus B19. Viruses, 11.","DOI":"10.3390\/v11070659"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e13652","DOI":"10.1111\/ctr.13652","article-title":"Post-transplant lymphoproliferative disorders, Epstein-Barr virus infection, and disease in solid organ transplantation: Guidelines from the American Society of Transplantation Infectious Diseases Community of Practice","volume":"33","author":"Allen","year":"2019","journal-title":"Clin. Transplant."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.jcv.2016.09.004","article-title":"Detection of parvovirus B19 DNA in blood: Viruses or DNA remnants?","volume":"84","author":"Backer","year":"2016","journal-title":"J. Clin. Virol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"e13396","DOI":"10.1111\/tid.13396","article-title":"Coinfection rates and clinical outcome data for cytomegalovirus and Epstein-Barr virus in post-transplant patients: A systematic review of the literature","volume":"22","author":"Baker","year":"2020","journal-title":"Transpl. Infect. Dis."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1007\/s00705-015-2363-9","article-title":"Human anelloviruses: An update of molecular, epidemiological and clinical aspects","volume":"160","author":"Spandole","year":"2015","journal-title":"Arch. Virol."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Moustafa, A., Xie, C., Kirkness, E., Biggs, W., Wong, E., Turpaz, Y., Bloom, K., Delwart, E., Nelson, K.E., and Venter, J.C. (2017). The blood DNA virome in 8000 humans. PLOS Pathog., 13.","DOI":"10.1371\/journal.ppat.1006292"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"104871","DOI":"10.1016\/j.jcv.2021.104871","article-title":"Torque teno virus loads after kidney transplantation predict allograft rejection but not viral infection","volume":"140","author":"Wunderink","year":"2021","journal-title":"J. Clin. Virol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/j.trre.2019.03.004","article-title":"Torque-Teno virus viral load as a potential endogenous marker of immune function in solid organ transplantation","volume":"33","author":"Rezahosseini","year":"2019","journal-title":"Transplant. Rev."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1016\/j.cell.2008.02.028","article-title":"Next-Generation Sequencing: The Race Is On","volume":"132","year":"2008","journal-title":"Cell"}],"container-title":["Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-0817\/11\/2\/236\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T22:17:26Z","timestamp":1760134646000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-0817\/11\/2\/236"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,2,11]]},"references-count":29,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2022,2]]}},"alternative-id":["pathogens11020236"],"URL":"https:\/\/doi.org\/10.3390\/pathogens11020236","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.07.14.21260507","asserted-by":"object"}]},"ISSN":["2076-0817"],"issn-type":[{"value":"2076-0817","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,2,11]]}}}