{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T06:03:46Z","timestamp":1791266626223,"version":"4.1.0"},"reference-count":54,"publisher":"American Society for Microbiology","issue":"17","license":[{"start":{"date-parts":[[2015,8,3]],"date-time":"2015-08-03T00:00:00Z","timestamp":1438560000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"},{"start":{"date-parts":[[2015,9,1]],"date-time":"2015-09-01T00:00:00Z","timestamp":1441065600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Virol"],"published-print":{"date-parts":[[2015,9]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            Enterovirus A71 (EV-A71) is a major cause of hand, foot, and mouth disease (HFMD) and is particularly prevalent in parts of Southeast Asia, affecting thousands of children and infants each year. Revealing the evolutionary and epidemiological dynamics of EV-A71 through time and space is central to understanding its outbreak potential. We generated the full genome sequences of 200 EV-A71 strains sampled from various locations in Viet Nam between 2011 and 2013 and used these sequence data to determine the evolutionary history and phylodynamics of EV-A71 in Viet Nam, providing estimates of the effective reproduction number (R\n            <jats:sub>e<\/jats:sub>\n            ) of the infection through time. In addition, we described the phylogeography of EV-A71 throughout Southeast Asia, documenting patterns of viral gene flow. Accordingly, our analysis reveals that a rapid genogroup switch from C4 to B5 likely took place during 2012 in Viet Nam. We show that the R\n            <jats:sub>e<\/jats:sub>\n            of subgenogroup C4 decreased during the time frame of sampling, whereas that of B5 increased and remained &gt;1 at the end of 2013, corresponding to a rise in B5 prevalence. Our study reveals that the subgenogroup B5 virus that emerged into Viet Nam is closely related to variants that were responsible for large epidemics in Malaysia and Taiwan and therefore extends our knowledge regarding its associated area of endemicity. Subgenogroup B5 evidently has the potential to cause more widespread outbreaks across Southeast Asia.\n          <\/jats:p>\n          <jats:p>\n            <jats:bold>IMPORTANCE<\/jats:bold>\n            EV-A71 is one of many viruses that cause HFMD, a common syndrome that largely affects infants and children. HFMD usually causes only mild illness with no long-term consequences. Occasionally, however, severe infection may arise, especially in very young children, causing neurological complications and even death. EV-A71 is highly contagious and is associated with the most severe HFMD cases, with large and frequent epidemics of the virus recorded worldwide. Although major advances have been made in the development of a potential EV-A71 vaccine, there is no current prevention and little is known about the patterns and dynamics of EV-A71 spread. In this study, we utilize full-length genome sequence data obtained from HFMD patients in Viet Nam, a geographical region where the disease has been endemic since 2003, to characterize the phylodynamics of this important emerging virus.\n          <\/jats:p>","DOI":"10.1128\/jvi.00706-15","type":"journal-article","created":{"date-parts":[[2015,6,18]],"date-time":"2015-06-18T02:46:26Z","timestamp":1434595586000},"page":"8871-8879","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":50,"title":["Phylodynamics of Enterovirus A71-Associated Hand, Foot, and Mouth Disease in Viet Nam"],"prefix":"10.1128","volume":"89","author":[{"given":"Jemma L.","family":"Geoghegan","sequence":"first","affiliation":[{"name":"Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Le Van","family":"Tan","sequence":"additional","affiliation":[{"name":"Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Denise","family":"K\u00fchnert","sequence":"additional","affiliation":[{"name":"Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland"},{"name":"Swiss Institute of Bioinformatics, Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca A.","family":"Halpin","sequence":"additional","affiliation":[{"name":"J. Craig Venter Institute, Rockville, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xudong","family":"Lin","sequence":"additional","affiliation":[{"name":"J. Craig Venter Institute, Rockville, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ari","family":"Simenauer","sequence":"additional","affiliation":[{"name":"J. Craig Venter Institute, Rockville, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Asmik","family":"Akopov","sequence":"additional","affiliation":[{"name":"J. Craig Venter Institute, Rockville, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suman R.","family":"Das","sequence":"additional","affiliation":[{"name":"J. Craig Venter Institute, Rockville, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy B.","family":"Stockwell","sequence":"additional","affiliation":[{"name":"J. Craig Venter Institute, Rockville, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susmita","family":"Shrivastava","sequence":"additional","affiliation":[{"name":"J. Craig Venter Institute, Rockville, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nghiem My","family":"Ngoc","sequence":"additional","affiliation":[{"name":"Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Le Thi Tam","family":"Uyen","sequence":"additional","affiliation":[{"name":"Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nguyen Thi Kim","family":"Tuyen","sequence":"additional","affiliation":[{"name":"Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tran Tan","family":"Thanh","sequence":"additional","affiliation":[{"name":"Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vu Thi Ty","family":"Hang","sequence":"additional","affiliation":[{"name":"Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Phan Tu","family":"Qui","sequence":"additional","affiliation":[{"name":"Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nguyen Thanh","family":"Hung","sequence":"additional","affiliation":[{"name":"Children's Hospital 1, Ho Chi Minh City, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Truong Huu","family":"Khanh","sequence":"additional","affiliation":[{"name":"Children's Hospital 1, Ho Chi Minh City, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Le Quoc","family":"Thinh","sequence":"additional","affiliation":[{"name":"Children's Hospital 1, Ho Chi Minh City, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Le Nguyen Thanh","family":"Nhan","sequence":"additional","affiliation":[{"name":"Children's Hospital 1, Ho Chi Minh City, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hoang Minh Tu","family":"Van","sequence":"additional","affiliation":[{"name":"Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Do Chau","family":"Viet","sequence":"additional","affiliation":[{"name":"Children's Hospital 2, Ho Chi Minh City, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ha Manh","family":"Tuan","sequence":"additional","affiliation":[{"name":"Children's Hospital 2, Ho Chi Minh City, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ho Lu","family":"Viet","sequence":"additional","affiliation":[{"name":"Children's Hospital 2, Ho Chi Minh City, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tran Tinh","family":"Hien","sequence":"additional","affiliation":[{"name":"Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nguyen Van Vinh","family":"Chau","sequence":"additional","affiliation":[{"name":"Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guy","family":"Thwaites","sequence":"additional","affiliation":[{"name":"Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam"},{"name":"Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bryan T.","family":"Grenfell","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA"},{"name":"Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tanja","family":"Stadler","sequence":"additional","affiliation":[{"name":"Swiss Institute of Bioinformatics, Lausanne, Switzerland"},{"name":"Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David E.","family":"Wentworth","sequence":"additional","affiliation":[{"name":"Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward C.","family":"Holmes","sequence":"additional","affiliation":[{"name":"Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H. Rogier","family":"Van Doorn","sequence":"additional","affiliation":[{"name":"Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam"},{"name":"Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1136\/jech-2014-203836"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2458-6-180"},{"key":"e_1_3_3_4_2","volume-title":"National Institutes of Health","author":"National Institutes of Health","year":"2015","unstructured":"National Institutes of Health. 2015. IDWR surveillance data table. National Institutes of Health, Bethesda, MD. http:\/\/www.nih.go.jp\/niid\/en\/survaillance-data-table-english.html."},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJM199909233411301"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(13)61049-1"},{"key":"e_1_3_3_7_2","volume-title":"WPRO hand, foot and mouth disease situation update","author":"World Health Organization","year":"2012","unstructured":"World Health Organization. 2012. WPRO hand, foot and mouth disease situation update. World Health Organization, Geneva, Switzerland."},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(12)61201-X"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(10)70194-8"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid1812.120929"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1186\/1743-422X-7-94"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01019-09"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(74)91684-5"},{"key":"e_1_3_3_14_2","first-page":"609","article-title":"Enterovirus type 71 infection in Melbourne","volume":"51","author":"Kennett ML","year":"1974","unstructured":"Kennett ML, Birch CJ, Lewis FA, Yung AP, Locarnini SA, Gust ID. 1974. Enterovirus type 71 infection in Melbourne. Bull World Health Organ 51:609\u2013615.","journal-title":"Bull World Health Organ"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF01317504"},{"key":"e_1_3_3_16_2","first-page":"284","article-title":"Epidemiological, clinical, and pathomorphological characteristics of epidemic poliomyelitis-like disease caused by enterovirus 71","volume":"23","author":"Shindarov LM","year":"1979","unstructured":"Shindarov LM, Chumakov MP, Voroshilova MK, Bojinov S, Vasilenko SM, Iordanov I, Kirov ID, Kamenov E, Leshchinskaya EV, Mitov G, Robinson IA, Sivchev S, Staikov S. 1979. Epidemiological, clinical, and pathomorphological characteristics of epidemic poliomyelitis-like disease caused by enterovirus 71. J Hyg Epidemiol Microbiol Immunol 23:284\u2013295.","journal-title":"J Hyg Epidemiol Microbiol Immunol"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF01314873"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1159\/000148922"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1136\/adc.55.8.583"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.06065-11"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid1311.070632"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0025662"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0100545"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1303224"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1304923"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.78.2.855-867.2004"},{"key":"e_1_3_3_27_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.80.1.483-493.2006"},{"key":"e_1_3_3_28_2","volume-title":"2011-2014: Emerging disease surveillance and response: hand, foot and mouth disease updates by year","author":"World Health Organization","year":"2014","unstructured":"World Health Organization. 2014. 2011-2014: Emerging disease surveillance and response: hand, foot and mouth disease updates by year. World Health Organization, Geneva, Switzerland."},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.3.2.120"},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jviromet.2015.02.011"},{"key":"e_1_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0096051"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq429"},{"key":"e_1_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mss075"},{"key":"e_1_3_3_34_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msn090"},{"key":"e_1_3_3_35_2","unstructured":"Rambaut A Drummond A. 2007. Tracer version 1.4. http:\/\/beast.bio.edac.uk\/Tracer."},{"key":"e_1_3_3_36_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2007.08.001"},{"key":"e_1_3_3_37_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1207965110"},{"key":"e_1_3_3_38_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0021116"},{"key":"e_1_3_3_39_2","doi-asserted-by":"publisher","DOI":"10.1097\/INF.0b013e3182116e95"},{"key":"e_1_3_3_40_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid1501.080264"},{"key":"e_1_3_3_41_2","doi-asserted-by":"publisher","DOI":"10.1007\/s12250-011-3195-8"},{"key":"e_1_3_3_42_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00630-09"},{"key":"e_1_3_3_43_2","volume-title":"World Health Organization","author":"WHO","year":"2015","unstructured":"WHO. 2015. Emerging disease surveillance and response: hand, foot and mouth disease (HFMD). World Health Organization, Geneva, Switzerland. http:\/\/www.wpro.who.int\/emerging_diseases\/HFMD\/en\/."},{"key":"e_1_3_3_44_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0080942"},{"key":"e_1_3_3_45_2","doi-asserted-by":"publisher","DOI":"10.1099\/vir.0.019695-0"},{"key":"e_1_3_3_46_2","doi-asserted-by":"publisher","DOI":"10.1186\/1743-422X-7-277"},{"key":"e_1_3_3_47_2","doi-asserted-by":"publisher","DOI":"10.1097\/INF.0b013e3181e52945"},{"key":"e_1_3_3_48_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0002067"},{"key":"e_1_3_3_49_2","doi-asserted-by":"publisher","DOI":"10.4269\/ajtmh.1952.1.30"},{"key":"e_1_3_3_50_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.virusres.2011.09.022"},{"key":"e_1_3_3_51_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.vaccine.2009.03.060"},{"key":"e_1_3_3_52_2","doi-asserted-by":"publisher","DOI":"10.1097\/EDE.0b013e318231d67a"},{"key":"e_1_3_3_53_2","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.aje.a009924"},{"key":"e_1_3_3_54_2","first-page":"167","article-title":"Duration of enterovirus shedding in stool","volume":"34","author":"Chung P-W","year":"2001","unstructured":"Chung P-W, Huang Y-C, Chang L-Y, Lin T-Y, Ning H-C. 2001. Duration of enterovirus shedding in stool. J Microbiol Immunol Infect 34:167\u2013170.","journal-title":"J Microbiol Immunol Infect"},{"key":"e_1_3_3_55_2","volume-title":"A guide to clinical management and public health response for hand, foot and mouth disease (HFMD)","author":"World Health Organization","year":"2011","unstructured":"World Health Organization. 2011. A guide to clinical management and public health response for hand, foot and mouth disease (HFMD). World Health Organization, Geneva, Switzerland."}],"container-title":["Journal of Virology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JVI.00706-15","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JVI.00706-15","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,5]],"date-time":"2022-03-05T15:52:20Z","timestamp":1646495540000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JVI.00706-15"}},"subtitle":[],"editor":[{"given":"A.","family":"Garc\u00eda-Sastre","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2015,9]]},"references-count":54,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2015,9]]}},"alternative-id":["10.1128\/JVI.00706-15"],"URL":"https:\/\/doi.org\/10.1128\/jvi.00706-15","relation":{},"ISSN":["0022-538X","1098-5514"],"issn-type":[{"value":"0022-538X","type":"print"},{"value":"1098-5514","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,9]]},"assertion":[{"value":"2015-03-16","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2015-06-07","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2015-08-03","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}