Molecular characteristics of the whole genome of CVA6 Enterovirus from Herpangina in Yancheng City in 2018
Objective To characterize the molecular epidemiology of coxsackievirus A6(CVA6)strains in Yancheng City.Methods The whole genome sequences of the enterovirus identified as CVA6 type in Yancheng City were amplified by reverse tran-scription polymerase chain reaction.The amplified products were purified and sequenced,and corresponding bioinformatics softwares were used to conduct nucleotide and amino acid sequence alignment,molecular evolutionary tree construction,and recombination analy-sis.Results In 2018,a total of 107 cases of suspected Herpangina were detected in Yancheng,and 79 cases resulting of positive En-terovirus nucleic acid amplification,with a positive rate of 73.83％.The positive rates of CVA6,CVA16,and other enteroviruses were 5.06％,50.63％,44.30％,respectively;while EV71 subtype wa not identified.The 3 strains of 2018 herpetic pharyngitis,3 strains of 2018 hand,foot,and mouth disease(HFMD,from pre peak,mid peak,and post peak),and one representative strain of 2017 HFMD CVA6 strains were selected for whole genome sequencing analysis.The phylogenetic tree analysis showed that 7 Yancheng strains of CVA6 be-longed to B2 evolutionary sub-branch in the evolutionary branch of B.The 3 Yancheng strains of Herpangina clustered with 2 Yancheng strains of HFMD in 2018 formed an evolutionary sub-branch;while 2 strains of HMFD(1 from 2017 and 1 from 2018)clustered into an independent evolutionary sub-branch to form 2 chains of transmission.A strain of Herpangina and 1 strain of HFMD CVA6 from each of the 2 evolutionary branches were selected to conduct molecular evolutionary recombination analysis;no obvious recombination source was identified.Conclusions The pathogenic spectrum of Herpangina cases in Yancheng city in 2018 showed genetic diversity and the genotype of CVA6 was the predominant epidemic strain,which may share common origin with HFMD srtrain.No recombination occurred in Yancheng strains.
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