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