{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,31]],"date-time":"2026-10-31T22:54:45Z","timestamp":1793487285993,"version":"4.5.0"},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,8,25]],"date-time":"2016-08-25T00:00:00Z","timestamp":1472083200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2016,8,25]],"date-time":"2016-08-25T00:00:00Z","timestamp":1472083200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"publisher","award":["KL2TR000143"],"award-info":[{"award-number":["KL2TR000143"]}],"id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005002","name":"California Department of Public Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005002","name":"California Department of Public Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000030","name":"Centers for Disease Control and Prevention","doi-asserted-by":"publisher","award":["U60OE000103"],"award-info":[{"award-number":["U60OE000103"]}],"id":[{"id":"10.13039\/100000030","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000030","name":"Centers for Disease Control and Prevention","doi-asserted-by":"publisher","award":["U60OE000103"],"award-info":[{"award-number":["U60OE000103"]}],"id":[{"id":"10.13039\/100000030","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007100","name":"Sandler Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007100","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007100","name":"Sandler Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007100","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010246","name":"William K. Bowes, Jr. Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010246","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Genome Med"],"published-print":{"date-parts":[[2016,12]]},"DOI":"10.1186\/s13073-016-0344-6","type":"journal-article","created":{"date-parts":[[2016,8,25]],"date-time":"2016-08-25T04:30:21Z","timestamp":1472099421000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":183,"title":["Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens"],"prefix":"10.1186","volume":"8","author":[{"given":"Thuy","family":"Doan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael R.","family":"Wilson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily D.","family":"Crawford","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric D.","family":"Chow","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lillian M.","family":"Khan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristeene A.","family":"Knopp","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian D.","family":"O\u2019Donovan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongxiang","family":"Xia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jill K.","family":"Hacker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jay M.","family":"Stewart","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John A.","family":"Gonzales","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nisha R.","family":"Acharya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph L.","family":"DeRisi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2016,8,25]]},"reference":[{"issue":"9","key":"344_CR1","doi-asserted-by":"publisher","first-page":"1761","DOI":"10.1016\/j.ophtha.2013.02.020","volume":"120","author":"S Sugita","year":"2013","unstructured":"Sugita S, Ogawa M, Shimizu N, et al. Use of a comprehensive polymerase chain reaction system for diagnosis of ocular infectious diseases. Ophthalmology. 2013;120(9):1761\u20138.","journal-title":"Ophthalmology"},{"key":"344_CR2","doi-asserted-by":"publisher","unstructured":"Taravati P, Lam D, Van Gelder RN. Role of molecular diagnostics in ocular microbiology. Curr Ophthalmol Rep. 2013;1(4). doi: 10.1007\/s40135-013-0025-1 .","DOI":"10.1007\/s40135-013-0025-1"},{"key":"344_CR3","doi-asserted-by":"crossref","unstructured":"Endophthalmitis Vitrectomy Study Collaboration. Results of the Endophthalmitis Vitrectomy Study. A randomized trial of immediate vitrectomy and of intravenous antibiotics for the treatment of postoperative bacterial endophthalmitis. Endophthalmitis Vitrectomy Study Group. Arch Ophthalmol. 1995;113(12):1479\u201396.","DOI":"10.1001\/archopht.1995.01100120009001"},{"issue":"25","key":"344_CR4","doi-asserted-by":"publisher","first-page":"2423","DOI":"10.1056\/NEJMoa1500306","volume":"372","author":"JB Varkey","year":"2015","unstructured":"Varkey JB, Shantha JG, Crozier I, et al. Persistence of Ebola virus in ocular fluid during convalescence. N Engl J Med. 2015;372(25):2423\u20137.","journal-title":"N Engl J Med"},{"key":"344_CR5","doi-asserted-by":"crossref","unstructured":"de Paula Freitas B, de Oliveira Dias JR, Prazeres J, et al. Ocular findings in infants with microcephaly associated with presumed Zika virus congenital infection in Salvador, Brazil. JAMA Ophthalmol. 2016;134(5):529\u2013535.","DOI":"10.1001\/jamaophthalmol.2016.0267"},{"key":"344_CR6","doi-asserted-by":"crossref","unstructured":"Wilson MR, Shanbhag NM, Reid MJ, et al. Diagnosing Balamuthia mandrillaris encephalitis with metagenomic deep sequencing. Ann Neurol. 2015;78(5):722\u201330.","DOI":"10.1002\/ana.24499"},{"issue":"25","key":"344_CR7","doi-asserted-by":"publisher","first-page":"2408","DOI":"10.1056\/NEJMoa1401268","volume":"370","author":"MR Wilson","year":"2014","unstructured":"Wilson MR, Naccache SN, Samayoa E, et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med. 2014;370(25):2408\u201317.","journal-title":"N Engl J Med"},{"issue":"11","key":"344_CR8","doi-asserted-by":"crossref","first-page":"1695","DOI":"10.1093\/cid\/civ670","volume":"61","author":"TR Pak","year":"2015","unstructured":"Pak TR, Kasarskis A. How next-generation sequencing and multiscale data analysis will transform infectious disease management. Clin Infect Dis. 2015;61(11):1695\u2013702.","journal-title":"Clin Infect Dis"},{"key":"344_CR9","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1186\/s13059-016-0904-5","volume":"17","author":"W Gu","year":"2016","unstructured":"Gu W, Crawford ED, O\u2019Donovan BD, Wilson MR, Chow ED, Retallack H, DeRisi JL. Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications. Genome Biol. 2016;17:41.","journal-title":"Genome Biol"},{"issue":"1","key":"344_CR10","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15\u201321.","journal-title":"Bioinformatics"},{"issue":"5","key":"344_CR11","doi-asserted-by":"publisher","first-page":"865","DOI":"10.1534\/g3.113.005967","volume":"3","author":"JG Ruby","year":"2013","unstructured":"Ruby JG, Bellare P, Derisi JL. PRICE: software for the targeted assembly of components of (Meta) genomic sequence data. G3 (Bethesda). 2013;3(5):865\u201380.","journal-title":"G3 (Bethesda)"},{"issue":"23","key":"344_CR12","doi-asserted-by":"publisher","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","volume":"28","author":"L Fu","year":"2012","unstructured":"Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28(23):3150\u20132.","journal-title":"Bioinformatics"},{"issue":"3","key":"344_CR13","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1109\/TIT.1977.1055714","volume":"23","author":"J Ziv","year":"1977","unstructured":"Ziv J, Lempel A. A universal algorithm for sequential data compression. IEEE Trans Inf Theory. 1977;23(3):337\u201343.","journal-title":"IEEE Trans Inf Theory"},{"issue":"4","key":"344_CR14","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357\u20139.","journal-title":"Nat Methods"},{"issue":"7","key":"344_CR15","doi-asserted-by":"publisher","first-page":"873","DOI":"10.1093\/bioinformatics\/btq057","volume":"26","author":"TD Wu","year":"2010","unstructured":"Wu TD, Nacu S. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics. 2010;26(7):873\u201381.","journal-title":"Bioinformatics"},{"issue":"1","key":"344_CR16","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1093\/bioinformatics\/btr595","volume":"28","author":"Y Zhao","year":"2012","unstructured":"Zhao Y, Tang H, Ye Y. RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics. 2012;28(1):125\u20136.","journal-title":"Bioinformatics"},{"issue":"9","key":"344_CR17","doi-asserted-by":"publisher","first-page":"2847","DOI":"10.1128\/JCM.00289-07","volume":"45","author":"Z Zhu","year":"2007","unstructured":"Zhu Z, Xu W, Abernathy ES, et al. Comparison of four methods using throat swabs to confirm rubella virus infection. J Clin Microbiol. 2007;45(9):2847\u201352.","journal-title":"J Clin Microbiol"},{"issue":"12","key":"344_CR18","doi-asserted-by":"publisher","first-page":"2107","DOI":"10.1002\/jmv.23935","volume":"86","author":"P Namuwulya","year":"2014","unstructured":"Namuwulya P, Abernathy E, Bukenya H, et al. Phylogenetic analysis of rubella viruses identified in Uganda, 2003-2012. J Med Virol. 2014;86(12):2107\u201313.","journal-title":"J Med Virol"},{"key":"344_CR19","unstructured":"Standardization of the nomenclature for genetic characteristics of wild-type rubella viruses. Wkly Epidemiol Rec. 2005;80(14):126\u201332."},{"key":"344_CR20","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1016\/j.jcv.2015.06.084","volume":"69","author":"E Abernathy","year":"2015","unstructured":"Abernathy E, Peairs RR, Chen MH, Icenogle J, Namdari H. Genomic characterization of a persistent rubella virus from a case of Fuch\u2019 uveitis syndrome in a 73\u00a0year old man. J Clin Virol. 2015;69:104\u20139.","journal-title":"J Clin Virol"},{"key":"344_CR21","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1186\/1743-422X-10-32","volume":"10","author":"E Abernathy","year":"2013","unstructured":"Abernathy E, Chen MH, Bera J, et al. Analysis of whole genome sequences of 16 strains of rubella virus from the United States, 1961-2009. Virol J. 2013;10:32.","journal-title":"Virol J"},{"key":"344_CR22","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1186\/1471-2148-10-8","volume":"10","author":"A Dereeper","year":"2010","unstructured":"Dereeper A, Audic S, Claverie JM, Blanc G. BLAST-EXPLORER helps you building datasets for phylogenetic analysis. BMC Evol Biol. 2010;10:8.","journal-title":"BMC Evol Biol"},{"issue":"Web Server issu","key":"344_CR23","doi-asserted-by":"publisher","first-page":"W465","DOI":"10.1093\/nar\/gkn180","volume":"36","author":"A Dereeper","year":"2008","unstructured":"Dereeper A, Guignon V, Blanc G, et al. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 2008;36(Web Server issue):W465\u20139.","journal-title":"Nucleic Acids Res"},{"key":"344_CR24","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1186\/1471-2105-5-113","volume":"5","author":"RC Edgar","year":"2004","unstructured":"Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinforma. 2004;5:113.","journal-title":"BMC Bioinforma"},{"key":"344_CR25","doi-asserted-by":"publisher","first-page":"7999","DOI":"10.1038\/srep07999","volume":"5","author":"Z Zhu","year":"2015","unstructured":"Zhu Z, Rivailler P, Abernathy E, et al. Evolutionary analysis of rubella viruses in mainland China during 2010-2012: endemic circulation of genotype 1E and introductions of genotype 2B. Sci Rep. 2015;5:7999.","journal-title":"Sci Rep"},{"issue":"9","key":"344_CR26","doi-asserted-by":"publisher","first-page":"e44954","DOI":"10.1371\/journal.pone.0044954","volume":"7","author":"D Lee","year":"2012","unstructured":"Lee D, Das Gupta J, Gaughan C, et al. In-depth investigation of archival and prospectively collected samples reveals no evidence for XMRV infection in prostate cancer. PLoS One. 2012;7(9):e44954.","journal-title":"PLoS One"},{"issue":"9984","key":"344_CR27","doi-asserted-by":"publisher","first-page":"2297","DOI":"10.1016\/S0140-6736(14)60539-0","volume":"385","author":"N Lambert","year":"2015","unstructured":"Lambert N, Strebel P, Orenstein W, Icenogle J, Poland GA. Rubella. Lancet. 2015;385(9984):2297\u2013307.","journal-title":"Lancet"},{"issue":"1","key":"344_CR28","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1016\/j.ajo.2004.02.055","volume":"138","author":"CD Quentin","year":"2004","unstructured":"Quentin CD, Reiber H. Fuchs heterochromic cyclitis: rubella virus antibodies and genome in aqueous humor. Am J Ophthalmol. 2004;138(1):46\u201354.","journal-title":"Am J Ophthalmol"},{"issue":"4","key":"344_CR29","doi-asserted-by":"publisher","first-page":"479","DOI":"10.1016\/j.ajo.2009.06.007","volume":"148","author":"ET Cunningham Jr","year":"2009","unstructured":"Cunningham Jr ET, Baglivo E. Fuchs heterochromic iridocyclitis--syndrome, disease, or both? Am J Ophthalmol. 2009;148(4):479\u201381.","journal-title":"Am J Ophthalmol"},{"issue":"3","key":"344_CR30","doi-asserted-by":"publisher","first-page":"424","DOI":"10.1016\/j.ajo.2007.05.026","volume":"144","author":"AD Birnbaum","year":"2007","unstructured":"Birnbaum AD, Tessler HH, Schultz KL, et al. Epidemiologic relationship between fuchs heterochromic iridocyclitis and the United States rubella vaccination program. Am J Ophthalmol. 2007;144(3):424\u20138.","journal-title":"Am J Ophthalmol"},{"issue":"1","key":"344_CR31","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1016\/j.ajo.2005.07.078","volume":"141","author":"JD de Groot-Mijnes","year":"2006","unstructured":"de Groot-Mijnes JD, de Visser L, Rothova A, Schuller M, van Loon AM, Weersink AJ. Rubella virus is associated with fuchs heterochromic iridocyclitis. Am J Ophthalmol. 2006;141(1):212\u20134.","journal-title":"Am J Ophthalmol"},{"issue":"8","key":"344_CR32","doi-asserted-by":"publisher","first-page":"e1005114","DOI":"10.1371\/journal.ppat.1005114","volume":"11","author":"G Dunn","year":"2015","unstructured":"Dunn G, Klapsa D, Wilton T, Stone L, Minor PD, Martin J. Twenty-eight years of poliovirus replication in an immunodeficient individual: impact on the global polio eradication initiative. PLoS Pathog. 2015;11(8):e1005114.","journal-title":"PLoS Pathog"},{"issue":"Suppl 2","key":"344_CR33","doi-asserted-by":"publisher","first-page":"S593","DOI":"10.1093\/infdis\/jir420","volume":"204","author":"SE Reef","year":"2011","unstructured":"Reef SE, Redd SB, Abernathy E, Kutty P, Icenogle JP. Evidence used to support the achievement and maintenance of elimination of rubella and congenital rubella syndrome in the United States. J Infect Dis. 2011;204 Suppl 2:S593\u20137.","journal-title":"J Infect Dis"},{"key":"344_CR34","unstructured":"Pan American Health Organization. Americas region is declared the world\u2019s first to eliminate rubella. 2015. Available from: http:\/\/www.paho.org\/us\/index.php?option=com_content&view=article&id=135%3Aamericas-region-free-of-rubella&Itemid=0&lang=en . Accessed 22 Aug 2016."}],"updated-by":[{"DOI":"10.1186\/s13073-016-0377-x","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2016,11,22]],"date-time":"2016-11-22T00:00:00Z","timestamp":1479772800000}}],"container-title":["Genome Medicine"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13073-016-0344-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s13073-016-0344-6\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13073-016-0344-6","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13073-016-0344-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,10]],"date-time":"2025-06-10T09:53:25Z","timestamp":1749549205000},"score":1,"resource":{"primary":{"URL":"https:\/\/genomemedicine.biomedcentral.com\/articles\/10.1186\/s13073-016-0344-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,8,25]]},"references-count":34,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2016,12]]}},"alternative-id":["344"],"URL":"https:\/\/doi.org\/10.1186\/s13073-016-0344-6","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/054148","asserted-by":"object"}]},"ISSN":["1756-994X"],"issn-type":[{"value":"1756-994X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,8,25]]},"assertion":[{"value":"28 May 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 August 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 August 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"90"}}