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Background  The transmission rate seasonality is an important index for transmission dynamics in many childhood infections, and has been widely studied in industrialized countries. However, it has been neglected in the study of pathogens in China.    Methods  To understand the transmission dynamics of hand, foot and mouth disease (HFMD), we examined the transmission rate seasonality of HFMD in three provinces, Henan, Anhui and Chongqing, in China, using a dynamical stochastic SIR model. We investigated potential driving factors, including school terms, the Chinese Spring Festival period, meteorological factors and population flux for their effects on the HFMD transmission seasonality using multiple regression models.    Results  The transmission rate of HFMD had complex seasonality with one large major peak in March and one small peak in autumn. School terms, the Chinese Spring Festival period, population flux and meteorological factors had combined effects on the HFMD transmission seasonality in mainland China. The school terms reflects the seasonal contact rate in Children, while the population flux and the Chinese Spring Festival period reflect the seasonal contact rate in population. They drove HFMD transmission rate seasonality in different time periods of the year in China. Contact rate seasonality in population dominated effects on HFMD transmission in February and March. The dramatic increase in transmission rate during February coincides with the Chinese Spring Festival period and high population flux in this month. The contact rate seasonality in children dominated effects on the transmission in the other months of the year in Chongqing. Meteorological factors can not solely explain the seasonality in HFMD transmission in mainland China; however, they may have combined effects with school terms and the highway passenger traffic on the transmission rate in Anhui during the fall semester.    Conclusion  The transmission rate of HFMD in three provinces in China had complex seasonality. The Chinese Spring Festival period, population flux and (or) school terms explained the majority of the transmission rate seasonality of HFMD, and they drove HFMD transmission rate seasonality in different time periods of the year. The Chinese Spring Festival period dominantly caused the dramatic increase of the HFMD transmission rate during February.    Electronic supplementary material  The online version of this article (10.1186/s12879-019-4153-6) contains supplementary material, which is available to authorized users.

The complex transmission seasonality of hand, foot, and mouth disease and its driving factors