Human enterovirus 71 (HEV-71) and coxsackievirus A16 (CV-A16) are the major etiological agent of hand-foot-and-mouth disease (HFMD). Both of them are genetically divided by molecular analysis into three groups, A, B, and C. Several studies showed that HEV-71 related HFMD has been linked to major outbreaks involving infections with severe neurological complications and death. Based on amplification of the partial VP1 region by semi-nested PCR, 3 and 25 of 50 samples obtained from 50 hospitalized pediatric patients during 2009 and 2010 were positive for HEV-71 and CV-A16, respectively. From this result, indicated an annual prevalence of 6% and 50%. Most of all positive samples were belonged to CV-A16-C. In a phylogenetic tree, based on the complete VP1 gene sequence, all three HEV-71 strains grouped into the B5, C1 and C4 genotype. The genetic heterogeneity of these strains culminated in amino acid substitutions within the VP1, VP2 and VP3 regions. The changes of amino acids sequences of the VP1 regions of CV-A16 were restored. The sequence analysis of HEV-71 and CV-A16 strains revealed that there are nucleotide changes clustered in the internal ribosome entry site (IRES) element of the 5́-untranslated region (5́-UTR). This amino acid difference is located in the finger domain of the viral RNA-dependent RNA polymerase 3D (3Dpol).
