Impact of COVID-19 on the transmission dynamics of HFMD associated enterovirus serotypes in Japan: a modelling study of surveillance data

A notable decline in incidence of hand, foot, and mouth disease (HFMD) was observed globally since the beginning of the COVID-19 pandemic, indicating a change in the transmission dynamics of enteroviruses (EVs) causing HFMD. This study estimates the impact of COVID-19 non-pharmaceutical interventions (NPIs) on the transmission of EVs in Japan. Japan has a well-established sentinel surveillance system for enteroviruses and HFMD. A susceptible-infected-recovered stochastic transmission model was fitted to the time-series of weekly reported number of HFMD enterovirus A71 (EV-A71), coxsackievirus A16 (CVA16), and CVA6 cases from January 2005 to December 2024, to estimate the impact of government containment interventions during the COVID-19 pandemic. Compared to pre-pandemic levels, the transmission rate decreased by 7.86% (95%Credible Interval (CrI): 6.31%, 10.3%) for EV-A71, 12.0% (10.3%, 14.1%) for CVA16, and 20.1% (16.3%, 24.0%) for CVA6 on average from January 2020 to December 2022. The reduction in transmission rate during this period correlated with the COVID-19 Stringency Index, such that 49.3%, 19.9% and 25.5% of the reduction for each serotype respectively was explained by the index, with the biggest reductions occurring during ‘State of Emergency’ periods. Enterovirus serotypes with higher transmissibility ( R 0 ) and therefore, a younger mean age at infection, were estimated to experience a bigger reduction in transmission that was more strongly associated with COVID-19 non-pharmaceutical interventions captured by the Stringency Index. This has implications for the impact of NPIs on other viral pathogens. • Between January 2005 and December 2024, CVA6, CVA16 and EV-A71 were the predominant enterovirus serotypes causing HFMD in Japan, accounting for 88.9% of EV-positive HFMD cases. • The containment measures against COVID-19 in Japan significantly reduced the transmission of HFMD-related EV-A71, CVA16, and CVA6 by 7.86% (95% CrI: 6.31%, 10.3%), 12.0% (95% CrI: 10.3%, 14.1%) and 20.1% (95% CrI: 16.3%, 24.0%) on average from January 2020 to December 2022. • Enterovirus serotypes with higher transmissibility ( R 0 ) and therefore, a younger mean age at infection, were estimated to experience a more significant reduction in transmission. • Compared to pre-COVID-19, COVID-19 NPIs increased population susceptibility to HFMD-related enteroviruses, resulting in an extended interval between consecutive epidemics of six years for EV-A71, five years for CVA16, and three years for CVA6.