Complete nucleotide sequence of a human coxsackievirus A16 strain KMM08 isolated in Kunming, China in 2008 / 中华流行病学杂志

ABSTRACT

Objective To describe the genetic characterization of complete genome from a human coxsackievirus A16 (CA16) strain KMM08,isolated in Yunnan,China,in 2008.Methods By using RT-PCR,the seven fragments contained about 1000 nucleotides in the complete genome were sequenced.The sequences were aligned with other enterovirus sequences downloaded from GenBank using Mega 4.1,RDP3 and SimPlot 3.5.1 software.Results As in other human enterovirus,its genome was 7409 nucleotides in length,encoding for 2193 amino acids.KMM08 strain was closely related to other reference strains of B genotype.In the complete genome,the homology of nucleotide and amino acid among the eleven CA16 isolated strains were 79.0％-98.2％ and 94.5％-99.3％,respectively.The rates of homology were 79.1％ and 94.8％ when comparing with that of G10 strains and 78.7％ and 89.0％ comparing with that of BrCr strains,respectively.SZ-HK08-3 strain had high homology when compared to other strains.In different segment of genome,the rates of homology were 97.0％-99.0％ and 98.0％-100.0％ when compared with that of SZ-HK08-3 strains,respectively.The rates of homology were 74.2％-86.9％ and 90.9％-97.0％ when compared with that of G10 strains,respectively and were 65.0％-84.9％ and 71.0％-95.2％ when compared with that of BrCr strains.Data from Phylogenetic analysis showed that KMM08 belong to genotype B.The putative recombinant Tainan-5079-98 was detected positive with RDP3 and SimPlot 3.5.1.Conclusion KMM08 strains isolated in Yunnan in 2008 belonged to B genotype of coxsackivirus A16.The possible occurrence of inter-typic recombination would involve EV71 and CA16.