{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T01:57:43Z","timestamp":1780624663968,"version":"3.54.1"},"reference-count":44,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2020,1,1]],"date-time":"2020-01-01T00:00:00Z","timestamp":1577836800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"}],"funder":[{"name":"NSW Ministry of Health Public Health Pathogen Genomics Partnership"},{"name":"SPHERE Triple I Clinical Academic Group Seed Funding"},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Motor Neurone Diseases Research Institute of Australia"},{"name":"Sydney Children\u2019s Hospital Foundation"},{"DOI":"10.13039\/501100000942","name":"Brain Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000942","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008888","name":"Thyne Reid Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008888","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005614","name":"Biogen","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005614","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Library of Medicine of the National Institutes of Health"}],"content-domain":{"domain":["clinicalkey.jp","clinicalkey.com","clinicalkey.es","clinicalkey.fr","clinicalkey.com.au","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Clinical Virology"],"published-print":{"date-parts":[[2020,1]]},"DOI":"10.1016\/j.jcv.2019.104216","type":"journal-article","created":{"date-parts":[[2019,11,17]],"date-time":"2019-11-17T06:48:11Z","timestamp":1573973291000},"page":"104216","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":8,"special_numbering":"C","title":["Next generation sequencing of human enterovirus strains from an outbreak of enterovirus A71 shows applicability to outbreak investigations"],"prefix":"10.1016","volume":"122","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6037-9305","authenticated-orcid":false,"given":"Sacha","family":"Stelzer-Braid","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6773-6325","authenticated-orcid":false,"given":"Matthew","family":"Wynn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Chatoor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5100-9724","authenticated-orcid":false,"given":"Matthew","family":"Scotch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vidiya","family":"Ramachandran","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hooi-Ling","family":"Teoh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle A.","family":"Farrar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hugo","family":"Sampaio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter Ian","family":"Andrews","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria E.","family":"Craig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C. Raina","family":"MacIntyre","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hemalatha","family":"Varadhan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alison","family":"Kesson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2993-6000","authenticated-orcid":false,"given":"Philip N.","family":"Britton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Newcombe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William D.","family":"Rawlinson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"6","key":"10.1016\/j.jcv.2019.104216_bib0005","doi-asserted-by":"crossref","first-page":"1204","DOI":"10.3201\/eid2506.181460","article-title":"Multirecombinant enterovirus A71 subgenogroup C1 isolates associated with neurologic disease, France, 2016-2017","volume":"25","author":"Ngangas","year":"2019","journal-title":"Emerg. Infect. Dis."},{"issue":"0","key":"10.1016\/j.jcv.2019.104216_bib0010","first-page":"e2082","article-title":"Global epidemiology of nonpolio enteroviruses causing severe neurological complications: a systematic review and meta-analysis","volume":"0","author":"Suresh","year":"2019","journal-title":"Rev. Med. Virol."},{"issue":"11","key":"10.1016\/j.jcv.2019.104216_bib0015","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1016\/S1474-4422(10)70209-X","article-title":"Clinical features, diagnosis, and management of enterovirus 71","volume":"9","author":"Ooi","year":"2010","journal-title":"Lancet Neurol."},{"issue":"4","key":"10.1016\/j.jcv.2019.104216_bib0020","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1016\/S1473-3099(13)70342-6","article-title":"Epidemiological characteristics of hand-foot-and-mouth disease in China, 2008-2012","volume":"14","author":"Xing","year":"2014","journal-title":"Lancet Infect. Dis."},{"issue":"3","key":"10.1016\/j.jcv.2019.104216_bib0025","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1001\/jamaneurol.2015.4388","article-title":"Clinical characteristics and functional motor outcomes of enterovirus 71 neurological disease in children","volume":"73","author":"Teoh","year":"2016","journal-title":"JAMA Neurol."},{"issue":"11","key":"10.1016\/j.jcv.2019.104216_bib0030","doi-asserted-by":"crossref","first-page":"663","DOI":"10.5694\/mja14.00014","article-title":"An outbreak of enterovirus 71 in metropolitan Sydney: enhanced surveillance and lessons learnt","volume":"201","author":"Zander","year":"2014","journal-title":"Med. J. Aust."},{"issue":"9","key":"10.1016\/j.jcv.2019.104216_bib0035","doi-asserted-by":"crossref","first-page":"2910","DOI":"10.1128\/JCM.01172-12","article-title":"Development and assay of RNA transcripts of enterovirus species A to D, rhinovirus species a to C, and human parechovirus: assessment of assay sensitivity and specificity of real-time screening and typing methods","volume":"50","author":"McLeish","year":"2012","journal-title":"J. Clin. Microbiol."},{"issue":"45","key":"10.1016\/j.jcv.2019.104216_bib0040","doi-asserted-by":"crossref","first-page":"16","DOI":"10.2807\/1560-7917.ES.2017.22.45.16-00807","article-title":"Surveillance and laboratory detection for non-polio enteroviruses in the European Union\/European Economic Area, 2016","volume":"22","author":"Harvala","year":"2017","journal-title":"Eurosurveillance"},{"issue":"5","key":"10.1016\/j.jcv.2019.104216_bib0045","doi-asserted-by":"crossref","first-page":"1288","DOI":"10.1128\/JCM.37.5.1288-1293.1999","article-title":"Typing of human enteroviruses by partial sequencing of VP1","volume":"37","author":"Oberste","year":"1999","journal-title":"J. Clin. Microbiol."},{"issue":"9","key":"10.1016\/j.jcv.2019.104216_bib0050","first-page":"e104","article-title":"Molecular epidemiology of human enterovirus 71 at the origin of an epidemic of fatal hand, foot and mouth disease cases in Cambodia","volume":"5","author":"Duong","year":"2016","journal-title":"Emerg. Microbes Infect."},{"key":"10.1016\/j.jcv.2019.104216_bib0055","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.jcv.2017.07.004","article-title":"Retrospective use of next-generation sequencing reveals the presence of Enteroviruses in acute influenza-like illness respiratory samples collected in South\/South-East Asia during 2010-2013","volume":"94","author":"Rutvisuttinunt","year":"2017","journal-title":"J. Clin. Virol."},{"key":"10.1016\/j.jcv.2019.104216_bib0060","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.virol.2016.04.026","article-title":"Genetic characterization of Enterovirus 71 strains circulating in Vietnam in 2012","volume":"495","author":"Donato","year":"2016","journal-title":"Virology"},{"issue":"10","key":"10.1016\/j.jcv.2019.104216_bib0065","doi-asserted-by":"crossref","first-page":"5102","DOI":"10.1128\/JCM.43.10.5102-5110.2005","article-title":"Development of multiplex PCRs for detection of common viral pathogens and agents of congenital infections","volume":"43","author":"McIver","year":"2005","journal-title":"J. Clin. Microbiol."},{"issue":"2","key":"10.1016\/j.jcv.2019.104216_bib0070","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1128\/JCM.41.2.841-844.2003","article-title":"Diagnosis of enterovirus infection by genus-specific PCR and enzyme-linked immunosorbent assays","volume":"41","author":"Craig","year":"2003","journal-title":"J. Clin. Microbiol."},{"issue":"2","key":"10.1016\/j.jcv.2019.104216_bib0075","doi-asserted-by":"crossref","DOI":"10.1093\/ve\/vey020","article-title":"A complex mosaic of enteroviruses shapes community-acquired hand, foot and mouth disease transmission and evolution within a single hospital","volume":"4","author":"Cobbin","year":"2018","journal-title":"Virus Evol."},{"issue":"1","key":"10.1016\/j.jcv.2019.104216_bib0080","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.jmii.2014.11.013","article-title":"Predicting severe enterovirus 71 infection: age, comorbidity, and parental behavior matter","volume":"50","author":"Huang","year":"2017","journal-title":"J. Microbiol., Immunol., Infect. = Wei mian yu gan ran za zhi"},{"key":"10.1016\/j.jcv.2019.104216_bib0085","series-title":"Manila WHO Regional Office for the Western Pacific","article-title":"A Guide to clinical management and public health response for hand, foot and mouth disease (HFMD)","author":"(WHO) WHO","year":"2011"},{"issue":"1","key":"10.1016\/j.jcv.2019.104216_bib0090","doi-asserted-by":"crossref","first-page":"11889","DOI":"10.1038\/s41598-018-30322-y","article-title":"Amplification and next generation sequencing of near full-length human enteroviruses for identification and characterisation from clinical samples","volume":"8","author":"Isaacs","year":"2018","journal-title":"Sci. Rep."},{"issue":"3","key":"10.1016\/j.jcv.2019.104216_bib0095","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"issue":"12","key":"10.1016\/j.jcv.2019.104216_bib0100","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1093\/bioinformatics\/bts199","article-title":"Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data","volume":"28","author":"Kearse","year":"2012","journal-title":"Bioinformatics"},{"issue":"22","key":"10.1016\/j.jcv.2019.104216_bib0105","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice","volume":"22","author":"Thompson","year":"1994","journal-title":"Nucleic Acids Res."},{"issue":"3","key":"10.1016\/j.jcv.2019.104216_bib0110","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/sysbio\/syq010","article-title":"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0","volume":"59","author":"Guindon","year":"2010","journal-title":"Syst. Biol."},{"issue":"1","key":"10.1016\/j.jcv.2019.104216_bib0115","doi-asserted-by":"crossref","DOI":"10.1093\/ve\/vey016","article-title":"Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10","volume":"4","author":"Suchard","year":"2018","journal-title":"Virus Evol."},{"issue":"9","key":"10.1016\/j.jcv.2019.104216_bib0120","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1000520","article-title":"Bayesian phylogeography finds its roots","volume":"5","author":"Lemey","year":"2009","journal-title":"PLoS Comput. Biol."},{"issue":"3","key":"10.1016\/j.jcv.2019.104216_bib0125","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1016\/j.meegid.2007.08.001","article-title":"Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty","volume":"8","author":"Parker","year":"2008","journal-title":"Infect. Genet. Evol."},{"issue":"1","key":"10.1016\/j.jcv.2019.104216_bib0130","doi-asserted-by":"crossref","DOI":"10.1093\/ve\/vev003","article-title":"RDP4: detection and analysis of recombination patterns in virus genomes","volume":"1","author":"Martin","year":"2015","journal-title":"Virus Evol."},{"issue":"1","key":"10.1016\/j.jcv.2019.104216_bib0135","doi-asserted-by":"crossref","first-page":"4","DOI":"10.7774\/cevr.2017.6.1.4","article-title":"Enterovirus 71 infection and vaccines","volume":"6","author":"Yi","year":"2017","journal-title":"Clin. Exp. Vaccine Res."},{"key":"10.1016\/j.jcv.2019.104216_bib0140","doi-asserted-by":"crossref","first-page":"38451","DOI":"10.1038\/srep38451","article-title":"Characterization of enterovirus 71 infection and associated outbreak of hand, foot, and mouth disease in Shawo of China in 2012","volume":"6","author":"Liu","year":"2016","journal-title":"Sci. Rep."},{"key":"10.1016\/j.jcv.2019.104216_bib0145","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1186\/s12985-015-0308-2","article-title":"Enterovirus 71 infection in children with hand, foot, and mouth disease in Shanghai, China: epidemiology, clinical feature and diagnosis","volume":"12","author":"Wang","year":"2015","journal-title":"Virol. J."},{"key":"10.1016\/j.jcv.2019.104216_bib0150","unstructured":"Statistics ABo. 4102.0 - Australian Social Trends, 2014 2014 [cited 2018 26th July]. Available from: http:\/\/www.abs.gov.au\/ausstats\/abs@.nsf\/Lookup\/4102.0main+features102014#SYDNEY."},{"issue":"3","key":"10.1016\/j.jcv.2019.104216_bib0155","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0004562","article-title":"Cyclical patterns of hand, foot and mouth disease caused by enterovirus A71 in Malaysia","volume":"10","author":"NikNadia","year":"2016","journal-title":"PLoS Negl. Trop. Dis."},{"issue":"1","key":"10.1016\/j.jcv.2019.104216_bib0160","doi-asserted-by":"crossref","first-page":"79","DOI":"10.3201\/eid1501.080264","article-title":"Enterovirus 71 outbreak, Brunei","volume":"15","author":"AbuBakar","year":"2009","journal-title":"Emerg. Infect. Dis."},{"issue":"6404","key":"10.1016\/j.jcv.2019.104216_bib0165","doi-asserted-by":"crossref","first-page":"800","DOI":"10.1126\/science.aat6777","article-title":"Serotype-specific immunity explains the incidence of diseases caused by human enteroviruses","volume":"361","author":"Pons-Salort","year":"2018","journal-title":"Science"},{"key":"10.1016\/j.jcv.2019.104216_bib0170","doi-asserted-by":"crossref","first-page":"k5246","DOI":"10.1136\/bmj.k5246","article-title":"Outbreaks of acute flaccid myelitis in the US","volume":"363","author":"Stelzer-Braid","year":"2018","journal-title":"BMJ"},{"issue":"7","key":"10.1016\/j.jcv.2019.104216_bib0175","first-page":"199","article-title":"Enterovirus 71 outbreak in Western Australia associated with acute flaccid paralysis. Preliminary report","volume":"23","author":"McMinn","year":"1999","journal-title":"Commun. Dis. Intell."},{"issue":"7","key":"10.1016\/j.jcv.2019.104216_bib0180","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1097\/00006454-198807000-00007","article-title":"Outbreak of enterovirus 71 infection in Victoria, Australia, with a high incidence of neurologic involvement","volume":"7","author":"Gilbert","year":"1988","journal-title":"Pediatr. Infect. Dis. J."},{"issue":"6","key":"10.1016\/j.jcv.2019.104216_bib0185","first-page":"609","article-title":"Enterovirus type 71 infection in Melbourne","volume":"51","author":"Kennett","year":"1974","journal-title":"Bull. World Health Organ."},{"issue":"3","key":"10.1016\/j.jcv.2019.104216_bib0190","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1097\/01.PCC.0000074274.58997.FE","article-title":"Neurogenic pulmonary edema in enterovirus 71 encephalitis is not uniformly fatal but causes severe morbidity in survivors","volume":"4","author":"Prager","year":"2003","journal-title":"Pediatr. Crit. Care Med."},{"issue":"2","key":"10.1016\/j.jcv.2019.104216_bib0195","first-page":"E161","article-title":"Australian national enterovirus reference laboratory annual report, 2014","volume":"41","author":"Roberts","year":"2017","journal-title":"Commun. Dis. Intell. Q. Rep."},{"key":"10.1016\/j.jcv.2019.104216_bib0200","series-title":"Enterovirus Surveillance Guidelines: Guidelines for Enterovirus Surveillance in Support of the Polio Eradication Initiative","author":"Europe WHOROf","year":"2015"},{"issue":"9","key":"10.1016\/j.jcv.2019.104216_bib0205","doi-asserted-by":"crossref","first-page":"3163","DOI":"10.1128\/JCM.02447-10","article-title":"Stability of hepatitis C virus, HIV, and hepatitis B virus nucleic acids in plasma samples after long-term storage at -20 degrees C and -70 degrees C","volume":"49","author":"Baleriola","year":"2011","journal-title":"J. Clin. Microbiol."},{"issue":"1","key":"10.1016\/j.jcv.2019.104216_bib0210","doi-asserted-by":"crossref","DOI":"10.3390\/v8010010","article-title":"Direct identification of enteroviruses in cerebrospinal fluid of patients with suspected meningitis by nested PCR amplification","volume":"8","author":"Krasota","year":"2016","journal-title":"Viruses"},{"issue":"21","key":"10.1016\/j.jcv.2019.104216_bib0215","first-page":"468","article-title":"Progress toward polio eradication--Worldwide, 2013-2014","volume":"63","author":"Moturi","year":"2014","journal-title":"MMWR Morb. Mortal. Wkly. Rep."},{"key":"10.1016\/j.jcv.2019.104216_bib0220","doi-asserted-by":"crossref","DOI":"10.1080\/21645515.2019.1581539","article-title":"Enterovirus A71 vaccine effectiveness in preventing enterovirus A71 infection among medically-attended hand, foot, and mouth disease cases, Beijing, China","author":"Wang","year":"2019","journal-title":"Hum. Vaccin. Immunother."}],"container-title":["Journal of Clinical Virology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S138665321930246X?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S138665321930246X?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2021,2,3]],"date-time":"2021-02-03T20:29:13Z","timestamp":1612384153000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S138665321930246X"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,1]]},"references-count":44,"alternative-id":["S138665321930246X"],"URL":"https:\/\/doi.org\/10.1016\/j.jcv.2019.104216","relation":{},"ISSN":["1386-6532"],"issn-type":[{"value":"1386-6532","type":"print"}],"subject":[],"published":{"date-parts":[[2020,1]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Next generation sequencing of human enterovirus strains from an outbreak of enterovirus A71 shows applicability to outbreak investigations","name":"articletitle","label":"Article Title"},{"value":"Journal of Clinical Virology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jcv.2019.104216","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2019 Elsevier B.V. All rights reserved.","name":"copyright","label":"Copyright"}],"article-number":"104216"}}