Background and aim To investigated the epidemiological and etiological characteristic of Hand-Foot-Mouth disease in Chongqing, China from 2010 to 2013.

Methods Descriptive epidemiological methods were used to describe the epidemic characteristics of 3760 hospitalised cases with HFMD in Chongqing children’s hospital during 2010 to 2013. The pathogens from 830 stool samples were determined by nested RT-PCR and the molecular characteristics were analysed by the phylogenetic trees.

Results There were two epidemic peaks every year during 2010 to 2013 in Chongqing. One occurred from April to July and another occurred from October to December. Most (91.22%) of the patients were under 5 years old and 76.28% were < 3 years of age. The ratio of male to female cases was 1.60:1. The dominant pathogens were EV71 (58.47%) and CA16 (18.09%). The percentage of CA16 infection cases decreased from 31.23% to 4.67% and CA6 increased from 2.11% to 16.36% from 2010 to 2013. Phylogenetic analysis indicated that EV71 isolates in Chongqing belonged to 3 lineages in subgenotype C4a and CA16 isolates belonged to B1 (B1a and B1b). The molecular evolution of all the isolates from mild and severe cases were nearly identical.

Conclusions HFMD had two epidemic peaks each year in Chongqing from 2010 to 2013. The major of the patients were under 5 years old. And the percentage of males is higher than females. The pathogens are mainly EV71 C4a and CA16 B1, during 2010 to 2013. CA16 infection cases decreased while CA6 infection cases increased from 2010 to 2013.