Phylodynamics of enterovirus A71-associated hand, foot, and mouth disease in Viet Nam

Jemma L. Geoghegan, Le Van Tan, Denise Kühnert, Rebecca A. Halpin, Xudong Lin, Ari Simenauer, Asmik Akopov, Suman R. Das, Timothy B. Stockwell, Susmita Shrivastava, Nghiem My Ngoc, Le Thi Tam Uyen, Nguyen Thi Kim Tuyen, Tran Tan Thanh, Vu Thi Ty Hang, Phan Tu Qui, Nguyen Thanh Hung, Truong Huu Khanh, Le Quoc Thinh, Le Nguyen Thanh NhanHoang Minh Tu Van, Do Chau Viet, Ha Manh Tuan, Ho Lu Viet, Tran Tinh Hien, Nguyen Van Vinh Chau, Guy Thwaites, Bryan T. Grenfell, Tanja Stadler, David E. Wentworth, Edward C. Holmes, H. Rogier Van Doorn

Research output: Contribution to journalArticlepeer-review

49 Scopus citations


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 (Re) 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 Re of subgenogroup C4 decreased during the time frame of sampling, whereas that of B5 increased and remained >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.

Original languageEnglish (US)
Pages (from-to)8871-8879
Number of pages9
JournalJournal of virology
Issue number17
StatePublished - 2015

All Science Journal Classification (ASJC) codes

  • Insect Science
  • Virology
  • Microbiology
  • Immunology


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