{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T23:17:40Z","timestamp":1787786260739,"version":"build-2784847793"},"reference-count":47,"publisher":"Springer Science and Business Media LLC","issue":"7961","license":[{"start":{"date-parts":[[2023,3,30]],"date-time":"2023-03-30T00:00:00Z","timestamp":1680134400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2023,3,30]],"date-time":"2023-03-30T00:00:00Z","timestamp":1680134400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nature"],"published-print":{"date-parts":[[2023,5,18]]},"DOI":"10.1038\/s41586-023-05949-1","type":"journal-article","created":{"date-parts":[[2023,4,4]],"date-time":"2023-04-04T07:08:57Z","timestamp":1680592137000},"page":"574-580","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":114,"title":["Adeno-associated virus type 2 in US children with acute severe hepatitis"],"prefix":"10.1038","volume":"617","author":[{"given":"Venice","family":"Servellita","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8930-745X","authenticated-orcid":false,"given":"Alicia","family":"Sotomayor Gonzalez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daryl M.","family":"Lamson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abiodun","family":"Foresythe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hee Jae","family":"Huh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9152-5923","authenticated-orcid":false,"given":"Adam L.","family":"Bazinet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas H.","family":"Bergman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert L.","family":"Bull","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karla Y.","family":"Garcia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer S.","family":"Goodrich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sean P.","family":"Lovett","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kisha","family":"Parker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diana","family":"Radune","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"April","family":"Hatada","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chao-Yang","family":"Pan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyle","family":"Rizzo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. Bradford","family":"Bertumen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christina","family":"Morales","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul E.","family":"Oluniyi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jenny","family":"Nguyen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica","family":"Tan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Doug","family":"Stryke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rayah","family":"Jaber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew T.","family":"Leslie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zin","family":"Lyons","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hayden D.","family":"Hedman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Umesh","family":"Parashar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maureen","family":"Sullivan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelly","family":"Wroblewski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Steven","family":"Oberste","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacqueline E.","family":"Tate","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7872-316X","authenticated-orcid":false,"given":"Julia M.","family":"Baker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Sugerman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caelin","family":"Potts","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyan","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Preeti","family":"Chhabra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"Pediatric Hepatitis of Unknown Etiology Working Group","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivia","family":"Almendares","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neha","family":"Balachandran","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jordan E.","family":"Cates","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brandi","family":"Freeman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anita","family":"Kambhampati","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel","family":"Marine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Everardo","family":"Vega","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary E.","family":"Wikswo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erin R.","family":"McKeever","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Kelly","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julie A.","family":"Boom","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leila C.","family":"Sahni","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janet A.","family":"Englund","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eileen J.","family":"Klein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary A.","family":"Staat","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maeve","family":"Marsh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erin","family":"Ricketts","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua L.","family":"Clayton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia","family":"Cano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miriam","family":"Oseguera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Blattner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"L. Amanda","family":"Ingram","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henry","family":"Shiau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William","family":"Britt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luz Helena","family":"Gutierrez Sanchez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caroline","family":"Ciric","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christina A.","family":"Rostad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Vinj\u00e9","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hannah L.","family":"Kirking","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8630-427X","authenticated-orcid":false,"given":"Debra A.","family":"Wadford","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6249-8033","authenticated-orcid":false,"given":"R. Taylor","family":"Raborn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kirsten","family":"St. George","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2915-2094","authenticated-orcid":false,"given":"Charles Y.","family":"Chiu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,3,30]]},"reference":[{"key":"5949_CR1","doi-asserted-by":"publisher","DOI":"10.1186\/s12916-022-02471-5","volume":"20","author":"S Khader","year":"2022","unstructured":"Khader, S., Foster, I., Dagens, A., Norton, A. & Sigfrid, L. Severe acute hepatitis of unknown aetiology in children-what is known? BMC Med. 20, 280 (2022).","journal-title":"BMC Med."},{"key":"5949_CR2","unstructured":"Severe acute hepatitis of unknown aetiology in children - multi-country. WHO Disease Outbreak News https:\/\/www.who.int\/emergencies\/disease-outbreak-news\/item\/2022-DON400 (2022)."},{"key":"5949_CR3","doi-asserted-by":"publisher","first-page":"852","DOI":"10.15585\/mmwr.mm7126e1","volume":"71","author":"J Cates","year":"2022","unstructured":"Cates, J. et al. Interim analysis of acute hepatitis of unknown etiology in children aged <10 years - United States, October 2021-June 2022. MMWR Morb. Mortal. Wkly Rep. 71, 852\u2013858 (2022).","journal-title":"MMWR Morb. Mortal. Wkly Rep."},{"key":"5949_CR4","doi-asserted-by":"publisher","DOI":"10.1002\/hep.32682","author":"R Elsheikh","year":"2022","unstructured":"Elsheikh, R. et al. Acute hepatitis of unknown origin in children: Behind the statistics. Hepatology https:\/\/doi.org\/10.1002\/hep.32682 (2022).","journal-title":"Hepatology"},{"key":"5949_CR5","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa2206294","author":"LH Gutierrez Sanchez","year":"2022","unstructured":"Gutierrez Sanchez, L. H. et al. A case series of children with acute hepatitis and human adenovirus infection. N. Engl. J. Med. https:\/\/doi.org\/10.1056\/NEJMoa2206294 (2022).","journal-title":"N. Engl. J. Med."},{"key":"5949_CR6","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa2206704","author":"C Kelgeri","year":"2022","unstructured":"Kelgeri, C. et al. Clinical spectrum of children with acute hepatitis of unknown cause. N. Engl. J. Med. https:\/\/doi.org\/10.1056\/NEJMoa2206704 (2022).","journal-title":"N. Engl. J. Med."},{"key":"5949_CR7","doi-asserted-by":"publisher","first-page":"2200318","DOI":"10.2807\/1560-7917.ES.2022.27.15.2200318","volume":"27","author":"K Marsh","year":"2022","unstructured":"Marsh, K. et al. Investigation into cases of hepatitis of unknown aetiology among young children, Scotland, 1 January 2022 to 12 April 2022. Euro Surveill. 27, 2200318 (2022).","journal-title":"Euro Surveill."},{"key":"5949_CR8","unstructured":"Technical Report: Acute Hepatitis of Unknown Cause (CDC, 2022); https:\/\/www.cdc.gov\/ncird\/investigation\/hepatitis-unknown-cause\/technical-report.html."},{"key":"5949_CR9","doi-asserted-by":"publisher","first-page":"1459","DOI":"10.3390\/v14071459","volume":"14","author":"J Kager","year":"2022","unstructured":"Kager, J. et al. Fulminant adenoviral-induced hepatitis in immunosuppressed patients. Viruses 14, 1459 (2022).","journal-title":"Viruses"},{"key":"5949_CR10","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1128\/CMR.5.3.262","volume":"5","author":"JC Hierholzer","year":"1992","unstructured":"Hierholzer, J. C. Adenoviruses in the immunocompromised host. Clin. Microbiol. Rev. 5, 262\u2013274 (1992).","journal-title":"Clin. Microbiol. Rev."},{"key":"5949_CR11","doi-asserted-by":"publisher","first-page":"358","DOI":"10.1038\/s41573-019-0012-9","volume":"18","author":"D Wang","year":"2019","unstructured":"Wang, D., Tai, P. W. L. & Gao, G. Adeno-associated virus vector as a platform for gene therapy delivery. Nat. Rev. Drug Discov. 18, 358\u2013378 (2019).","journal-title":"Nat. Rev. Drug Discov."},{"key":"5949_CR12","doi-asserted-by":"publisher","first-page":"662","DOI":"10.3390\/v12060662","volume":"12","author":"AF Meier","year":"2020","unstructured":"Meier, A. F., Fraefel, C. & Seyffert, M. The interplay between adeno-associated virus and its helper viruses. Viruses 12, 662 (2020).","journal-title":"Viruses"},{"key":"5949_CR13","doi-asserted-by":"publisher","first-page":"6081","DOI":"10.1073\/pnas.0937739100","volume":"100","author":"G Gao","year":"2003","unstructured":"Gao, G. et al. Adeno-associated viruses undergo substantial evolution in primates during natural infections. Proc. Natl Acad. Sci. USA 100, 6081\u20136086 (2003).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"5949_CR14","doi-asserted-by":"publisher","unstructured":"Ho, A. et al. Adeno-associated virus 2 infection in children with non-A-E hepatitis. Nature https:\/\/doi.org\/10.1038\/s41586-023-05948-2 (2023).","DOI":"10.1038\/s41586-023-05948-2"},{"key":"5949_CR15","unstructured":"Recommendations for adenovirus testing and reporting of children with acute hepatitis of unknown etiology. CDC Health Alert Network https:\/\/emergency.cdc.gov\/han\/2022\/han00462.asp (2022)."},{"key":"5949_CR16","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1038\/s41576-019-0113-7","volume":"20","author":"CY Chiu","year":"2019","unstructured":"Chiu, C. Y. & Miller, S. A. Clinical metagenomics. Nat. Rev. Genet. 20, 341\u2013355 (2019).","journal-title":"Nat. Rev. Genet."},{"key":"5949_CR17","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1038\/s41564-019-0637-9","volume":"5","author":"X Deng","year":"2020","unstructured":"Deng, X. et al. Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance. Nat. Microbiol. 5, 443\u2013454 (2020).","journal-title":"Nat. Microbiol."},{"key":"5949_CR18","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-83642-x","volume":"11","author":"KW Kim","year":"2021","unstructured":"Kim, K. W. et al. Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing. Sci. Rep. 11, 3934 (2021).","journal-title":"Sci. Rep."},{"key":"5949_CR19","doi-asserted-by":"publisher","first-page":"a021550","DOI":"10.1101\/cshperspect.a021550","volume":"4","author":"F Negro","year":"2014","unstructured":"Negro, F. Hepatitis D virus coinfection and superinfection. Cold Spring Harb. Perspect. Med. 4, a021550 (2014).","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"5949_CR20","doi-asserted-by":"publisher","first-page":"1782","DOI":"10.1136\/gutjnl-2020-323888","volume":"70","author":"S Urban","year":"2021","unstructured":"Urban, S., Neumann-Haefelin, C. & Lampertico, P. Hepatitis D virus in 2021: virology, immunology and new treatment approaches for a difficult-to-treat disease. Gut 70, 1782\u20131794 (2021).","journal-title":"Gut"},{"key":"5949_CR21","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1136\/gutjnl-2019-318281","volume":"69","author":"T La Bella","year":"2020","unstructured":"La Bella, T. et al. Adeno-associated virus in the liver: natural history and consequences in tumour development. Gut 69, 737\u2013747 (2020).","journal-title":"Gut"},{"key":"5949_CR22","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1128\/CVI.05107-11","volume":"18","author":"R Calcedo","year":"2011","unstructured":"Calcedo, R. et al. Adeno-associated virus antibody profiles in newborns, children, and adolescents. Clin. Vaccine Immunol. 18, 1586\u20131588 (2011).","journal-title":"Clin. Vaccine Immunol."},{"key":"5949_CR23","doi-asserted-by":"publisher","first-page":"14781","DOI":"10.1128\/JVI.79.23.14781-14792.2005","volume":"79","author":"CL Chen","year":"2005","unstructured":"Chen, C. L. et al. Molecular characterization of adeno-associated viruses infecting children. J. Virol. 79, 14781\u201314792 (2005).","journal-title":"J. Virol."},{"key":"5949_CR24","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-17047-1","volume":"11","author":"HL Hsu","year":"2020","unstructured":"Hsu, H. L. et al. Structural characterization of a novel human adeno-associated virus capsid with neurotropic properties. Nat. Commun. 11, 3279 (2020).","journal-title":"Nat. Commun."},{"key":"5949_CR25","doi-asserted-by":"publisher","first-page":"1051","DOI":"10.1002\/jmv.21143","volume":"80","author":"L Chevret","year":"2008","unstructured":"Chevret, L. et al. Human herpesvirus-6 infection: a prospective study evaluating HHV-6 DNA levels in liver from children with acute liver failure. J. Med. Virol. 80, 1051\u20131057 (2008).","journal-title":"J. Med. Virol."},{"key":"5949_CR26","doi-asserted-by":"publisher","first-page":"1630","DOI":"10.1007\/s10620-014-3029-2","volume":"59","author":"JL Mellinger","year":"2014","unstructured":"Mellinger, J. L. et al. Epstein-Barr virus (EBV) related acute liver failure: a case series from the US Acute Liver Failure Study Group. Dig. Dis. Sci. 59, 1630\u20131637 (2014).","journal-title":"Dig. Dis. Sci."},{"key":"5949_CR27","doi-asserted-by":"publisher","first-page":"1872","DOI":"10.3390\/v14091872","volume":"14","author":"B Brooks","year":"2022","unstructured":"Brooks, B. et al. Epstein-Barr virus and human herpesvirus-6 reactivation in acute COVID-19 patients. Viruses 14, 1872 (2022).","journal-title":"Viruses"},{"key":"5949_CR28","doi-asserted-by":"publisher","unstructured":"Morfopoulou, S. et al. Genomic investigations of unexplained acute hepatitis in children. Nature https:\/\/doi.org\/10.1038\/s41586-023-06003-w (2023).","DOI":"10.1038\/s41586-023-06003-w"},{"key":"5949_CR29","doi-asserted-by":"publisher","first-page":"831","DOI":"10.1101\/gr.238170.118","volume":"29","author":"S Miller","year":"2019","unstructured":"Miller, S. et al. Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid. Genome Res. 29, 831\u2013842 (2019).","journal-title":"Genome Res."},{"key":"5949_CR30","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","volume":"30","author":"K Katoh","year":"2013","unstructured":"Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772\u2013780 (2013).","journal-title":"Mol. Biol. Evol."},{"key":"5949_CR31","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","volume":"32","author":"LT Nguyen","year":"2015","unstructured":"Nguyen, L. T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268\u2013274 (2015).","journal-title":"Mol. Biol. Evol."},{"key":"5949_CR32","unstructured":"QuickFacts: Alabama. US Census Bureau https:\/\/www.census.gov\/quickfacts\/AL (2021)."},{"key":"5949_CR33","doi-asserted-by":"publisher","first-page":"1539","DOI":"10.1093\/infdis\/jiab177","volume":"224","author":"MD Esona","year":"2021","unstructured":"Esona, M. D. et al. Rotavirus genotype trends and gastrointestinal pathogen detection in the United States, 2014-2016: results from the New Vaccine Surveillance Network. J. Infect. Dis. 224, 1539\u20131549 (2021).","journal-title":"J. Infect. Dis."},{"key":"5949_CR34","doi-asserted-by":"publisher","first-page":"228","DOI":"10.1002\/jmv.10382","volume":"70","author":"A Heim","year":"2003","unstructured":"Heim, A., Ebnet, C., Harste, G. & Pring-Akerblom, P. Rapid and quantitative detection of human adenovirus DNA by real-time PCR. J. Med. Virol. 70, 228\u2013239 (2003).","journal-title":"J. Med. Virol."},{"key":"5949_CR35","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1016\/j.jpeds.2008.07.057","volume":"154","author":"WH Lyman","year":"2009","unstructured":"Lyman, W. H. et al. Prospective study of etiologic agents of acute gastroenteritis outbreaks in child care centers. J. Pediatr. 154, 253\u2013257 (2009).","journal-title":"J. Pediatr."},{"key":"5949_CR36","doi-asserted-by":"publisher","first-page":"1587","DOI":"10.1007\/s00705-005-0722-7","volume":"151","author":"X Lu","year":"2006","unstructured":"Lu, X. & Erdman, D. D. Molecular typing of human adenoviruses by PCR and sequencing of a partial region of the hexon gene. Arch. Virol. 151, 1587\u20131602 (2006).","journal-title":"Arch. Virol."},{"key":"5949_CR37","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403\u2013410 (1990).","journal-title":"J. Mol. Biol."},{"key":"5949_CR38","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s00705-006-0842-8","volume":"152","author":"M Okada","year":"2007","unstructured":"Okada, M., Ogawa, T., Kubonoya, H., Yoshizumi, H. & Shinozaki, K. Detection and sequence-based typing of human adenoviruses using sensitive universal primer sets for the hexon gene. Arch. Virol. 152, 1\u20139 (2007).","journal-title":"Arch. Virol."},{"key":"5949_CR39","doi-asserted-by":"publisher","first-page":"2172","DOI":"10.1002\/jmv.22169","volume":"83","author":"M Dupuis","year":"2011","unstructured":"Dupuis, M. et al. Molecular detection of viral causes of encephalitis and meningitis in New York State. J. Med. Virol. 83, 2172\u20132181 (2011).","journal-title":"J. Med. Virol."},{"key":"5949_CR40","doi-asserted-by":"publisher","first-page":"1261","DOI":"10.1038\/nprot.2017.066","volume":"12","author":"J Quick","year":"2017","unstructured":"Quick, J. et al. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat. Protoc. 12, 1261\u20131276 (2017).","journal-title":"Nat. Protoc."},{"key":"5949_CR41","doi-asserted-by":"publisher","first-page":"1180","DOI":"10.1101\/gr.171934.113","volume":"24","author":"SN Naccache","year":"2014","unstructured":"Naccache, S. N. et al. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res. 24, 1180\u20131192 (2014).","journal-title":"Genome Res."},{"key":"5949_CR42","doi-asserted-by":"publisher","first-page":"1647","DOI":"10.1093\/bioinformatics\/bts199","volume":"28","author":"M Kearse","year":"2012","unstructured":"Kearse, M. et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647\u20131649 (2012).","journal-title":"Bioinformatics"},{"key":"5949_CR43","unstructured":"Bushnell, B. BBMap: a fast, accurate, splice-aware aligner. https:\/\/www.osti.gov\/servlets\/purl\/1241166 (2014)."},{"key":"5949_CR44","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).","journal-title":"Nat. Methods"},{"key":"5949_CR45","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-018-1618-7","volume":"20","author":"ND Grubaugh","year":"2019","unstructured":"Grubaugh, N. D. et al. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar. Genome Biol. 20, 8 (2019).","journal-title":"Genome Biol."},{"key":"5949_CR46","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1038\/s41592-019-0686-2","volume":"17","author":"P Virtanen","year":"2020","unstructured":"Virtanen, P. et al. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat. Methods 17, 261\u2013272 (2020).","journal-title":"Nat. Methods"},{"key":"5949_CR47","unstructured":"R Core Team. R: A Language and Environmental for Statistical Computing http:\/\/www.R-project.org (R Foundation for Statistical Computing, 2013)."}],"container-title":["Nature"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41586-023-05949-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-023-05949-1","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-023-05949-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,18]],"date-time":"2023-05-18T06:05:04Z","timestamp":1684389904000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41586-023-05949-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,3,30]]},"references-count":47,"journal-issue":{"issue":"7961","published-print":{"date-parts":[[2023,5,18]]}},"alternative-id":["5949"],"URL":"https:\/\/doi.org\/10.1038\/s41586-023-05949-1","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.742594072.793598384","asserted-by":"object"}]},"ISSN":["0028-0836","1476-4687"],"issn-type":[{"value":"0028-0836","type":"print"},{"value":"1476-4687","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,3,30]]},"assertion":[{"value":"11 September 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 March 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 March 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"C.Y.C. is a founder of Delve Bio and on the scientific advisory board for Delve Bio, Mammoth Biosciences, BiomeSense and Poppy Health. He is also a co-inventor on US patent 11380421, \u201cPathogen detection using next generation sequencing\u201d, under which algorithms for taxonomic classification, filtering and pathogen detection are used by SURPI+ software. C.Y.C. receives research support unrelated to this manuscript from Abbott Laboratories, Inc. The institution of C.A.R. has received financial support to conduct clinical research unrelated to this manuscript from BioFire Inc., GSK, Janssen, MedImmune, Merck, Moderna, Novavax, PaxVax, Pfizer, Regeneron and Sanofi-Pasteur. She is co-inventor of patented respiratory syncytial virus vaccine technology, which has been licensed to Meissa Vaccines, Inc. K.S.G. receives research support unrelated to this manuscript from Thermo-Fisher and has a royalty-generating collaborative agreement with Zeptometrix. The other authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"This content has been made available to all.","name":"free","label":"Free to read"}]}}