{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T03:34:47Z","timestamp":1789702487202,"version":"4.0.1"},"reference-count":25,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,9,14]],"date-time":"2016-09-14T00:00:00Z","timestamp":1473811200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2016,9,14]],"date-time":"2016-09-14T00:00:00Z","timestamp":1473811200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Acute encephalitis\/encephalopathy is a severe neurological syndrome that is occasionally associated with viral infection. Comprehensive virus detection assays are desirable because viral pathogens have not been identified in many cases. We evaluated the utility of next-generation sequencing (NGS) for detecting viruses in clinical samples of encephalitis\/encephalopathy patients. We first determined the sensitivity and quantitative performance of NGS by comparing the NGS-determined number of sequences of human herpesvirus-6 (HHV-6) in clinical serum samples with the HHV-6 load measured using real-time PCR. HHV-6 was measured as it occasionally causes neurologic disorders in children. The sensitivity of NGS for detection of HHV-6 sequences was equivalent to that of real-time PCR, and the number of HHV-6 reads was significantly correlated with HHV-6 load. Next, we investigated the ability of NGS to detect viral sequences in 18 pediatric patients with acute encephalitis\/encephalopathy of unknown etiology. A large number of Coxsackievirus A9 and mumps viral sequences were detected in the cerebrospinal fluid of 2 and 1 patients, respectively. In addition, Torque teno virus and Pepper mild mottle viral sequences were detected in the sera of one patient each. These data indicate that NGS is useful for detection of causative viruses in patients with pediatric encephalitis\/encephalopathy.<\/jats:p>","DOI":"10.1038\/srep33452","type":"journal-article","created":{"date-parts":[[2016,9,14]],"date-time":"2016-09-14T10:09:12Z","timestamp":1473847752000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":82,"title":["Identification of Viruses in Cases of Pediatric Acute Encephalitis and Encephalopathy Using Next-Generation Sequencing"],"prefix":"10.1038","volume":"6","author":[{"given":"Jun-ichi","family":"Kawada","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yusuke","family":"Okuno","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuka","family":"Torii","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryo","family":"Okada","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Satoshi","family":"Hayano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shotaro","family":"Ando","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yasuko","family":"Kamiya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seiji","family":"Kojima","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoshinori","family":"Ito","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2016,9,14]]},"reference":[{"key":"BFsrep33452_CR1","doi-asserted-by":"publisher","first-page":"1565","DOI":"10.1086\/509330","volume":"43","author":"CA Glaser","year":"2006","unstructured":"Glaser, C. A. et al. Beyond viruses: clinical profiles and etiologies associated with encephalitis. Clin Infect Dis 43, 1565\u20131577 (2006).","journal-title":"Clin Infect Dis"},{"key":"BFsrep33452_CR2","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1016\/j.braindev.2011.07.012","volume":"34","author":"A Hoshino","year":"2012","unstructured":"Hoshino, A. et al. Epidemiology of acute encephalopathy in Japan, with emphasis on the association of viruses and syndromes. Brain Dev 34, 337\u2013343 (2012).","journal-title":"Brain Dev"},{"key":"BFsrep33452_CR3","doi-asserted-by":"publisher","first-page":"e1485","DOI":"10.1371\/journal.pntd.0001485","volume":"6","author":"NL Yozwiak","year":"2012","unstructured":"Yozwiak, N. L. et al. Virus identification in unknown tropical febrile illness cases using deep sequencing. PLoS Negl Trop Dis 6, e1485 (2012).","journal-title":"PLoS Negl Trop Dis"},{"key":"BFsrep33452_CR4","doi-asserted-by":"publisher","first-page":"3722","DOI":"10.1128\/JCM.01641-14","volume":"52","author":"S Prachayangprecha","year":"2014","unstructured":"Prachayangprecha, S. et al. Exploring the potential of next-generation sequencing in detection of respiratory viruses. J Clin Microbiol 52, 3722\u20133730 (2014).","journal-title":"J Clin Microbiol"},{"key":"BFsrep33452_CR5","first-page":"1484","volume":"17","author":"LA Benjamin","year":"2011","unstructured":"Benjamin, L. A. et al. Human parvovirus 4 as potential cause of encephalitis in children, India. Emerg Infect Dis 17, 1484\u20131487 (2011).","journal-title":"Emerg Infect Dis"},{"key":"BFsrep33452_CR6","doi-asserted-by":"publisher","first-page":"e93993","DOI":"10.1371\/journal.pone.0093993","volume":"9","author":"BK Chan","year":"2014","unstructured":"Chan, B. K., Wilson, T., Fischer, K. F. & Kriesel, J. D. Deep sequencing to identify the causes of viral encephalitis. PloS One 9, e93993 (2014).","journal-title":"PloS One"},{"key":"BFsrep33452_CR7","doi-asserted-by":"publisher","first-page":"857","DOI":"10.1016\/j.jiac.2015.08.018","volume":"21","author":"N Kawashima","year":"2015","unstructured":"Kawashima, N. et al. Fulminant adenovirus hepatitis after hematopoietic stem cell transplant: Retrospective real-time PCR analysis for adenovirus DNA in two cases. J Infect Chemother 21, 857\u2013863 (2015).","journal-title":"J Infect Chemother"},{"key":"BFsrep33452_CR8","doi-asserted-by":"publisher","first-page":"13201","DOI":"10.1038\/srep13201","volume":"5","author":"L Vinner","year":"2015","unstructured":"Vinner, L. et al. Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing. Sci Rep 5, 13201 (2015).","journal-title":"Sci Rep"},{"key":"BFsrep33452_CR9","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/j.jviromet.2014.12.002","volume":"213","author":"L Li","year":"2015","unstructured":"Li, L. et al. Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent. J Virol Methods 213, 139\u2013146 (2015).","journal-title":"J Virol Methods"},{"key":"BFsrep33452_CR10","doi-asserted-by":"publisher","first-page":"1685","DOI":"10.1086\/592988","volume":"198","author":"AL Fowlkes","year":"2008","unstructured":"Fowlkes, A. L. et al. Enterovirus-associated encephalitis in the California encephalitis project, 1998\u20132005. J Infect Dis 198, 1685\u20131691 (2008).","journal-title":"J Infect Dis"},{"key":"BFsrep33452_CR11","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/j.biologicals.2004.10.003","volume":"33","author":"M Jose","year":"2005","unstructured":"Jose, M., Gajardo, R. & Jorquera, J. I. Stability of HCV, HIV-1 and HBV nucleic acids in plasma samples under long-term storage. Biologicals 33, 9\u201316 (2005).","journal-title":"Biologicals"},{"key":"BFsrep33452_CR12","doi-asserted-by":"publisher","first-page":"4147","DOI":"10.1128\/JCM.02659-12","volume":"50","author":"MR Hasan","year":"2012","unstructured":"Hasan, M. R., Tan, R., Al-Rawahi, G. N., Thomas, E. & Tilley, P. Short-term stability of pathogen-specific nucleic acid targets in clinical samples. J Clinical Microbiol 50, 4147\u20134150 (2012).","journal-title":"J Clinical Microbiol"},{"key":"BFsrep33452_CR13","doi-asserted-by":"publisher","first-page":"1807","DOI":"10.1056\/NEJM200106143442401","volume":"344","author":"D Nash","year":"2001","unstructured":"Nash, D. et al. The outbreak of West Nile virus infection in the New York City area in 1999. N Engl J Med 344, 1807\u20131814 (2001).","journal-title":"N Engl J Med"},{"key":"BFsrep33452_CR14","doi-asserted-by":"publisher","first-page":"1410","DOI":"10.1002\/jmv.21808","volume":"82","author":"S Kawabe","year":"2010","unstructured":"Kawabe, S. et al. Comparison of the levels of human herpesvirus 6 (HHV-6) DNA and cytokines in the cerebrospinal fluid and serum of children with HHV-6 encephalopathy. J Med Virol 82, 1410\u20131415 (2010).","journal-title":"J Med Virol"},{"key":"BFsrep33452_CR15","doi-asserted-by":"publisher","first-page":"690","DOI":"10.1086\/377101","volume":"188","author":"J Kawada","year":"2003","unstructured":"Kawada, J. et al. Systemic cytokine responses in patients with influenza-associated encephalopathy. J Infect Dis 188, 690\u2013698 (2003).","journal-title":"J Infect Dis"},{"key":"BFsrep33452_CR16","doi-asserted-by":"publisher","first-page":"1677","DOI":"10.1099\/vir.0.81670-0","volume":"87","author":"J Kawada","year":"2006","unstructured":"Kawada, J. et al. Analysis of gene-expression profiles by oligonucleotide microarray in children with influenza. J Gen Virol 87, 1677\u20131683 (2006).","journal-title":"J Gen Virol"},{"key":"BFsrep33452_CR17","doi-asserted-by":"publisher","first-page":"e10041","DOI":"10.1371\/journal.pone.0010041","volume":"5","author":"P Colson","year":"2010","unstructured":"Colson, P. et al. Pepper mild mottle virus, a plant virus associated with specific immune responses, Fever, abdominal pains, and pruritus in humans. PloS One 5, e10041 (2010).","journal-title":"PloS One"},{"key":"BFsrep33452_CR18","first-page":"1","volume":"331","author":"H Okamoto","year":"2009","unstructured":"Okamoto, H. History of discoveries and pathogenicity of TT viruses. Curr Top Microbiol Immunol 331, 1\u201320 (2009).","journal-title":"Curr Top Microbiol Immunol"},{"key":"BFsrep33452_CR19","doi-asserted-by":"publisher","first-page":"e1004437","DOI":"10.1371\/journal.ppat.1004437","volume":"10","author":"MJ Strong","year":"2014","unstructured":"Strong, M. J. et al. Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples. PLoS Pathogens 10, e1004437 (2014).","journal-title":"PLoS Pathogens"},{"key":"BFsrep33452_CR20","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.jviromet.2015.09.010","volume":"226","author":"K Perlejewski","year":"2015","unstructured":"Perlejewski, K. et al. Next-generation sequencing (NGS) in the identification of encephalitis-causing viruses: Unexpected detection of human herpesvirus 1 while searching for RNA pathogens. J Virol Methods 226, 1\u20136 (2015).","journal-title":"J Virol Methods"},{"key":"BFsrep33452_CR21","doi-asserted-by":"publisher","first-page":"1426","DOI":"10.1128\/JCM.01515-06","volume":"45","author":"K Wada","year":"2007","unstructured":"Wada, K. et al. Simultaneous quantification of Epstein-Barr virus, cytomegalovirus, and human herpesvirus 6 DNA in samples from transplant recipients by multiplex real-time PCR assay. J Clin Microbiol 45, 1426\u20131432 (2007).","journal-title":"J Clin Microbiol"},{"key":"BFsrep33452_CR22","doi-asserted-by":"publisher","first-page":"62","DOI":"10.7883\/yoken.67.62","volume":"67","author":"F Takeuchi","year":"2014","unstructured":"Takeuchi, F. et al. MePIC, metagenomic pathogen identification for clinical specimens. Jpn J Infectious Dis 67, 62\u201365 (2014).","journal-title":"Jpn J Infectious Dis"},{"key":"BFsrep33452_CR23","doi-asserted-by":"publisher","first-page":"465","DOI":"10.1016\/B978-0-12-407863-5.00021-6","volume":"531","author":"DH Huson","year":"2013","unstructured":"Huson, D. H. & Weber, N. Microbial community analysis using MEGAN. Methods Enzymol 531, 465\u2013485 (2013).","journal-title":"Methods Enzymol"},{"key":"BFsrep33452_CR24","doi-asserted-by":"publisher","first-page":"420","DOI":"10.1002\/jmv.10412","volume":"70","author":"I Thoelen","year":"2003","unstructured":"Thoelen, I. et al. Molecular typing and epidemiology of enteroviruses identified from an outbreak of aseptic meningitis in Belgium during the summer of 2000. J Med Virol 70, 420\u2013429 (2003).","journal-title":"J Med Virol"},{"key":"BFsrep33452_CR25","doi-asserted-by":"publisher","first-page":"1917","DOI":"10.1128\/JCM.02387-10","volume":"49","author":"M Kidokoro","year":"2011","unstructured":"Kidokoro, M., Tuul, R., Komase, K. & Nymadawa, P. Characterization of mumps viruses circulating in Mongolia: identification of a novel cluster of genotype H. J Clin Microbiol 49, 1917\u20131925 (2011).","journal-title":"J Clin Microbiol"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/srep33452.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/srep33452","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/srep33452.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,5]],"date-time":"2023-01-05T06:51:47Z","timestamp":1672901507000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/srep33452"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,9,14]]},"references-count":25,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2016,12,16]]}},"alternative-id":["BFsrep33452"],"URL":"https:\/\/doi.org\/10.1038\/srep33452","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,9,14]]},"assertion":[{"value":"17 March 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 August 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 September 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing financial interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"33452"}}