Sequence Feature Analysis Of VP1 Gene Of Coxsackievirus A16 From HFMD In Chongqing,2010-2015

Objectve:Through the analysis of the nucleotide sequence of coxsackievirus A16 VP1 with HFMD in Chongqing from 2010 to 2015,To understood the characteristics of CA16 VP1 gene in Chongqing in recent 6 years,and provide the basis for the relevant research about VP1 gene of CA16.Methods:Collect the stool samples from HFMD patients in Chongqing from 2010 to 2015,and detect the pathogen type.Specific primers were used to amplify and sequence these complete VP1 genes in our laboratory by nRTPCR.54 isolated strains were randomly selected to construct phylogenetic tree,and analyze the VP1 amino acid variation in Chongqing.Results:1.Phylogenetic tree showed that the virus isolates stains in Chongqing from 2010 to 2015 were all B1 subtypes,and there were two epidemic branches at the same time.The virus strains in 2014-2015 were all B1 b subtypes,and no B1 a was found on the shunt branch.Also the temporal clusters could be found in Chongqing,the annual epidemic distribution was different.2.In this study,we demonstrated a total of 8 amino acid variation sites,and 22 virus strains were found L5 M variation.Conclusion: From 2010 to 2015,Coxsackievirus A16 isolates stains were all B1 subtypes in Chongqing,and we could find two transmission chains circulating at the same time,with time clustering.two epidemic branches at the same time.The virus strains in 2014-2015 were all B1 b subtypes,suggesting that B1 b subtypes may gradually form independent dominant evolutionary branches in the process of common circulation and epidemic.We found 8 amino acid variation sites in virus strains,but there are no literatures which have reported the variation sites,and whether they affect the virulence of CA16 should be studied.