Molecular genotyping of the enterovirus for non-enterovirus 71 and non-coxsackievirus A16 in Yancheng area in 2016 and analysis of the characteristics of VP1 gene of coxsackievirus A6

Objective To study the pathogenic spectrum of the enterovirus for non-enterovirus 71 (non-EV71) and non-coxsackievirus A16(non-CVA16) for hand, foot and mouth disease (HFMD)in the city of Yancheng in 2016, and characterize the molecular epidemiology of the VP1 gene of coxsackievirus A6 strains. Methods The serotype of coxsackievirus A6 strains were identified by molecular subtyping. The sequences of the VP1 gene of coxsackievirus A6 strains were amplified through one step reverse transcription polymerose chain reaction (RT-PCR) method and the PCR products were sequenced. The sequences of nucleotide and amino of the VP1 gene of coxsackievirus A6 were analyzed and the evolutional tree was generated using bioinformatics software. Results There was significant difference among the three positive rates in EV71,CVA16 and non-EV71, non-CVA16(χ²=87.72,P<0.001).The strains of the enterovirus for non-EV71 and non-CVA16 were classified into seven genotypes (CVA4,CVA6,CVA10,Echovirus 3(E-3),E-9,E-13,Coxsackievirus B4(CVB4)) and belonged to human enterovirus A group and human enterovirus B group. Phylogenetic tree analysis showed that 56 strains of enterovirus coxsackievirus A6 in Yancheng area belonged to D3,D4 evolutionary sub-branches. Among them, 54 strains belonged to D4 evolutionary sub-branch, which was the mainstream sub-branch in china. Within the D4 sub-branch, 54 strains were clustered into numerous small sub-branches and away from the prototype Gdula strain. Conclusions The spectrum of pathogens causing HFMD epidemics in Yancheng area in 2016 was multifarious and the genotype of coxsackievirus A6 was the prevalent pathogen. D4 sub-branch of strains was the dominant evolutionary branch and formed multiple transmission chains.