{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T03:35:17Z","timestamp":1789702517931,"version":"4.0.1"},"reference-count":34,"publisher":"American Society of Tropical Medicine and Hygiene","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,9,7]]},"abstract":"<jats:p>Numerous pathogens cause respiratory infections with similar symptoms. Routine diagnostics detect only a limited number of pathogens, leaving a gap in respiratory illness etiology surveillance. This study evaluated next-generation sequencing for unbiased pathogen identification. Respiratory samples collected in Thailand, Philippines, Bhutan, and Nepal, that were negative by several molecular and immunofluorescence assays, underwent viral cultivation. Samples which demonstrated cytopathic effect in culture (<jats:italic>N<\/jats:italic> = 121) were extracted and tested by Luminex xTAG respiratory viral panel (RVP) assay and deep sequencing by Roche 454 FLX Titanium system. Using RVP assay, 52 (43%) samples were positive for enterovirus or rhinovirus and another three were positive for respiratory syncytial virus B, parainfluenza 4, and adenovirus. Deep sequencing confirmed the Luminex assay results and identified additional viral pathogens. Human enteroviruses, including <jats:italic>Enterovirus A<\/jats:italic> type 71 and 12 types of <jats:italic>Enterovirus B<\/jats:italic> (EV-B) were identified from a hospital in Bangkok. Phylogenetic and recombination analysis showed high correlation of VP1 gene-based phylogeny with genome-wide phylogeny and the frequent genetic exchange among EV-B viruses. The high number and diversity of enteroviruses in the hospital in Bangkok suggests prevalent existence. The metagenomic approach used in our study enabled comprehensive diagnoses of respiratory viruses.<\/jats:p>","DOI":"10.4269\/ajtmh.16-0062","type":"journal-article","created":{"date-parts":[[2016,6,29]],"date-time":"2016-06-29T17:10:39Z","timestamp":1467220239000},"page":"663-669","source":"Crossref","is-referenced-by-count":28,"title":["Metagenomics Study of Viral Pathogens in Undiagnosed Respiratory Specimens and Identification of Human Enteroviruses at a Thailand Hospital"],"prefix":"10.4269","volume":"95","author":[{"given":"Yanfei","family":"Zhou","sequence":"first","affiliation":[{"name":"1Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Fernandez","sequence":"additional","affiliation":[{"name":"2Department of Virology, U.S. Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"In-Kyu","family":"Yoon","sequence":"additional","affiliation":[{"name":"2Department of Virology, U.S. Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand."},{"name":"3International Vaccine Institute, Seoul, Republic of Korea."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sriluck","family":"Simasathien","sequence":"additional","affiliation":[{"name":"4Department of Pediatrics, Phramongkutklao Hospital, Bangkok, Thailand."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Veerachai","family":"Watanaveeradej","sequence":"additional","affiliation":[{"name":"4Department of Pediatrics, Phramongkutklao Hospital, Bangkok, Thailand."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Yang","sequence":"additional","affiliation":[{"name":"1Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Omely A.","family":"Marte-Salcedo","sequence":"additional","affiliation":[{"name":"1Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deidra J.","family":"Shuck-Lee","sequence":"additional","affiliation":[{"name":"1Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen J.","family":"Thomas","sequence":"additional","affiliation":[{"name":"1Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Hang","sequence":"additional","affiliation":[{"name":"1Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard G.","family":"Jarman","sequence":"additional","affiliation":[{"name":"1Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2795","reference":[{"issue":"(Suppl 2)","key":"ref1","series-title":"BMC Public Health","first-page":"S6","article-title":"Department of Defense influenza and other respiratory disease surveillance during the 2009 pandemic","volume":"11","author":"Burke","year":"2011"},{"key":"ref2","series-title":"Curr Opin Virol","first-page":"192","article-title":"Intervention strategies for emerging respiratory virus infections: policy and public health considerations","volume":"3","author":"Nguyen-Van-Tam","year":"2013"},{"key":"ref3","series-title":"Nat Rev Microbiol","first-page":"133","article-title":"The changing face of pathogen discovery and surveillance","volume":"11","author":"Lipkin","year":"2013"},{"key":"ref4","series-title":"Curr Opin Pulm Med","first-page":"271","article-title":"New respiratory viral infections","volume":"18","author":"Jartti","year":"2012"},{"key":"ref5","series-title":"Microbiol Mol Biol Rev","first-page":"363","article-title":"Microbe hunting. Microbiology and molecular biology reviews","volume":"74","author":"Lipkin","year":"2010"},{"key":"ref6","series-title":"J Clin Microbiol","first-page":"2238","article-title":"Evaluation of unbiased next-generation sequencing of RNA (RNA-seq) as a diagnostic method in influenza virus-positive respiratory samples","volume":"53","author":"Fischer","year":"2015"},{"key":"ref7","series-title":"PLoS One","first-page":"e7370","article-title":"Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals","volume":"4","author":"Willner","year":"2009"},{"key":"ref8","series-title":"J Gen Virol","first-page":"1853","article-title":"Application of next-generation sequencing technologies in virology","volume":"93","author":"Radford","year":"2012"},{"key":"ref9","series-title":"Int J Mol Sci","first-page":"7861","article-title":"Applications of next-generation sequencing technologies to diagnostic virology","volume":"12","author":"Barzon","year":"2011"},{"key":"ref10","series-title":"J Clin Virol","first-page":"96","article-title":"The use of next generation sequencing in the diagnosis and typing of respiratory infections","volume":"69","author":"Thorburn","year":"2015"},{"key":"ref11","series-title":"J Pathol","first-page":"217","article-title":"Tissue tropism, pathology and pathogenesis of enterovirus infection","volume":"235","author":"Muehlenbachs","year":"2014"},{"key":"ref12","series-title":"JAMA","first-page":"1290","article-title":"CDC tracking enterovirus D-68 outbreak causing severe respiratory illness in children in the Midwest","volume":"312","author":"Stephenson","year":"2014"},{"key":"ref13","series-title":"Handb Clin Neurol","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1016\/B978-0-444-53488-0.00018-3","article-title":"Enterovirus\/picornavirus infections","volume":"123","author":"Jubelt","year":"2014"},{"key":"ref14","series-title":"J Biomol Tech","first-page":"4","article-title":"Random amplification and pyrosequencing for identification of novel viral genome sequences","volume":"23","author":"Hang","year":"2012"},{"key":"ref15","series-title":"J Clin Virol","first-page":"121","article-title":"An automated genotyping tool for enteroviruses and noroviruses","volume":"51","author":"Kroneman","year":"2011"},{"key":"ref16","series-title":"Mol Biol Evol","first-page":"2725","article-title":"MEGA6: Molecular Evolutionary Genetics Analysis version 6.0","volume":"30","author":"Tamura","year":"2013"},{"key":"ref17","series-title":"Bioinformatics","first-page":"2462","article-title":"RDP3: a flexible and fast computer program for analyzing recombination","volume":"26","author":"Martin","year":"2010"},{"key":"ref18","series-title":"J Clin Microbiol","first-page":"1523","article-title":"Identification of dengue virus in respiratory specimens from a patient who had recently traveled from a region where dengue virus infection is endemic","volume":"45","author":"Tavakoli","year":"2007"},{"key":"ref19","series-title":"J Biomed Sci","first-page":"16","article-title":"Epidemiology and seroepidemiology of human enterovirus 71 among Thai populations","volume":"21","author":"Linsuwanon","year":"2014"},{"key":"ref20","series-title":"Lancet Infect Dis","first-page":"778","article-title":"Virology, epidemiology, pathogenesis, and control of enterovirus 71","volume":"10","author":"Solomon","year":"2010"},{"key":"ref21","series-title":"PLoS One","first-page":"e56341","article-title":"Complete genome analysis of the C4 subgenotype strains of enterovirus 71: predominant recombination C4 viruses persistently circulating in China for 14 years","volume":"8","author":"Zhang","year":"2013"},{"key":"ref22","series-title":"Genome Announc","first-page":"e00457-14","article-title":"Complete genome sequence of a human enterovirus 71 strain isolated from a fatal case in Shanghai, China, in 2012","volume":"2","author":"Wang","year":"2014"},{"key":"ref23","series-title":"J Virol","first-page":"855","article-title":"Evidence for frequent recombination within species human enterovirus B based on complete genomic sequences of all thirty-seven (sero)types","volume":"78","author":"Oberste","year":"2004"},{"key":"ref24","series-title":"LDhat 2.1: A Package for the Population Genetic Analysis of Recombination","author":"McVean","year":"2007"},{"key":"ref25","series-title":"PLoS Negl Trop Dis","first-page":"e1485","article-title":"Virus identification in unknown tropical febrile illness cases using deep sequencing","volume":"6","author":"Yozwiak","year":"2012"},{"key":"ref26","series-title":"N Engl J Med","first-page":"2408","article-title":"Actionable diagnosis of neuroleptospirosis by next-generation sequencing","volume":"370","author":"Wilson","year":"2014"},{"key":"ref27","series-title":"J Clin Virol","first-page":"346","article-title":"Next-generation sequencing technologies in diagnostic virology","volume":"58","author":"Barzon","year":"2013"},{"key":"ref28","series-title":"Virol J","first-page":"169","article-title":"Non-rhinovirus enteroviruses associated with respiratory infections in Peru (2005\u20132010)","volume":"11","author":"Huaman","year":"2014"},{"key":"ref29","series-title":"J Clin Virol","first-page":"181","article-title":"The relevance of respiratory viral infections in the exacerbations of chronic obstructive pulmonary disease: a systematic review","volume":"61","author":"Zwaans","year":"2014"},{"key":"ref30","series-title":"Infect Genet Evol","first-page":"404","article-title":"Phylogenetic designation of enterovirus 71 genotypes and subgenotypes using complete genome sequences","volume":"10","author":"Chan","year":"2010"},{"key":"ref31","series-title":"Virol J","first-page":"305","article-title":"Human rhinoviruses and enteroviruses in influenza-like illness in Latin America","volume":"10","author":"Garcia","year":"2013"},{"key":"ref32","series-title":"Int J Infect Dis","first-page":"e1245","article-title":"Newly emerging C group enteroviruses may elude diagnosis due to a divergent 5\u2032-UTR","volume":"17","author":"Richter","year":"2013"},{"key":"ref33","series-title":"J Clin Microbiol","first-page":"2698","article-title":"Sensitive, seminested PCR amplification of VP1 sequences for direct identification of all enterovirus (sero)types from original clinical specimens","volume":"44","author":"Nix","year":"2006"},{"key":"ref34","series-title":"PLoS One","first-page":"e90624","article-title":"Molecular comparison and evolutionary analyses of VP1 nucleotide sequences of new African human enterovirus 71 isolates reveal a wide genetic diversity","volume":"9","author":"Bessaud","year":"2014"}],"container-title":["The American Society of Tropical Medicine and Hygiene"],"original-title":[],"link":[{"URL":"https:\/\/www.ajtmh.org\/view\/journals\/tpmd\/95\/3\/article-p663.xml","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.ajtmh.org\/downloadpdf\/journals\/tpmd\/95\/3\/article-p663.xml","content-type":"text\/html","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/www.ajtmh.org\/downloadpdf\/journals\/tpmd\/95\/3\/article-p663.xml","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,7]],"date-time":"2024-08-07T21:57:27Z","timestamp":1723067847000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.ajtmh.org\/view\/journals\/tpmd\/95\/3\/article-p663.xml"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,9,7]]},"references-count":34,"journal-issue":{"issue":"3"},"URL":"https:\/\/doi.org\/10.4269\/ajtmh.16-0062","relation":{},"ISSN":["0002-9637","1476-1645"],"issn-type":[{"value":"0002-9637","type":"print"},{"value":"1476-1645","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,9,7]]}}}