ABSTRACT
<p><b>OBJECTIVE</b>To analyze the genetic characterization of the complete genome from a human coxsackievirus B3 strain A103/KM/09 isolated in Yunnan province, 2009.</p><p><b>METHODS</b>By using RT-PCR, all the eight fragments which containing about 1000 nucleotides and covering full viral genome, were sequenced. By using Mega 5.05,Geneious, RDP 3 and SimPlot 3.5.1 software, sequences were aligned with other enterovirus reference sequences. Phylogenetic and recombination analysis were also carried out.</p><p><b>RESULTS</b>The A103/KM/09 isolate genome showed 7389 nucleotides in length , encoding for 2185 amino acids. In the complete genome, the homology of nucleotide and amino acid among the seven coxsackievirus B3 isolates were 81.0%-88.0% and 95.7%-98.0%, respectively. There appeared 81.0% and 95.7% homology when compared with that of Nancy prototype strain. Results from the Phylogenetic analysis showed that the coxsackievirus B3 formed five distinct clades, I-V. Nucleotide divergence rates between clades were 16.2%-24.3% . The A103/KM/09 strain belonged to clade V. Clade V was further divided into four sub-clades,A-D. The nucleotide divergence between sub-clades was 4.3%-11.4%. Putative recombinant event for A103/ KM/09 was detected.</p><p><b>CONCLUSION</b>All coxsackievirus B3 isolates could be divided into five clades, with A103/KM/09 strain belonged to Clade V-D. Evolution of coxsackievirus B3 had occurred in China.</p>
Subject(s)
Child, Preschool , Humans , Male , Base Sequence , China , Epidemiology , Encephalitis, Viral , Epidemiology , Virology , Enterovirus B, Human , Genetics , Enterovirus Infections , Epidemiology , Virology , Genome, Viral , Phylogeny , Viral Proteins , GeneticsABSTRACT
Objective To analyze the genetic characterization of the complete genome from a human echovirus 6 (Echo6) strain KM57-09 isolated in Yunnan,China,in 2009.Methods Using the RT-PCR,eight fragments containing about 1000 nucleotides which covered the whole viral genome were sequenced.The sequences were aligned with other reference cnterovirus sequences downloaded from the GenBank,using Mega 5.05,RDP 3 and SimPlot 3.5.1 softwares.Results Similar to the other human cntcrovirus,KM57-09 isolate genome appeared to have 7419 nucleotides in length,encoding for 2191 amino acids.In the complete genome,the rates of homology on nucleotide and amino acid among the seven Echo6 isolates were 79.3％-80.2％ and 93.3％ 94.4％,respectively as well as 79.3％ and 93.6％ of the rates of homology when compared with that of D' Amor prototype strain.In different segment of genome.The 2C 3A genome region was most similar to the HN-2-E25 strain,the 5' UTR,VP4,3D and 3' UTR genomc region were most similar to the CoxB5-Henan2010.In the VP1 gene,the rates of homology on nuclcotide and amino acid among the China isolates were 80.0％-96.0％ and 95.8％-99.0％,respectively,and showed 77.6％-96.0％ and 95.2％-99.0％ of the rates on homology when compared to the other Echo6 reference strains isolated from other countries or areas,respectively.Results from phylogenetic analysis showed that the Echo6 formed five distinct groups,A-E.The KM57-09 strain belonged to clade E.The nucleotide divergence between clades was 15.6％-23.3％.The putative recombinant event for KM57-09 was detected with RDP 3,SimPlot 3.5.1 and 3D sequence phylogenetic analysis.Conclusion All the Echo6 isolates could be divided into five clades,the KM57-09 strain belonged to Clade E.The Echo6 strains isolated in China were contributed to several different chains of transmission.