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Objective: Genetic polymorphism on the carnitine palmitoyl transferase Ⅱ (CPT Ⅱ) gene has been reported as a susceptibility factor in a number of syndromes of acute encephalopathy with various infectious diseases, but evidence of its effect on Enterovirus 71 (EV71) infection is lacking.The goal of this study was to examine the relationship between Genetic polymorphism of CPT Ⅱ and severity of EV71 infection in a Chinese population.Methods:A case-control study was conducted to compare the distribution of genotype and genetic frequency of rs1799821, rs1799822, rs2229291 and rs7554022 gene polymorphisms among EV71-associated hand, foot and mouth disease (HFMD) patients (n=333), including mild cases (n=271), severe cases (n=62) and healthy control subjects (n=328) by using the improved multiplex ligasedetection reaction technology (iMLDRTM).Blood ATP levels were measured within 24h of admission and the convalescent phase.