ABSTRACT
To characterize the complete genome sequence of coxsackievirus B1 (CVB1) MSH/KM9/2009 strain isolated from Yunnan, China,2009. Eight overlapping clones covering the whole viral genome (excluding the poly-A tail) were obtained by RT-PCR and sequenced, and their nucleotide and amino acid sequences were compared with other known CVB1 strains. The genome of the CVB1 MSH/KM9/2009 strain had 7384 nucleotides in length, and contained a 741nt non-translated region (NTR) at the 5' end and a 94nt NTR at the 3' end. The entire open reading frame contained 6 549 nt, encoding a 2 183-aa polyprotein. In the coding region, there was no nucleotide deletion or insertion, but some changes of amino acid were unique. The complete genome sequence alignments showed that the CVB1 isolate MSH/KM9/2009 strain shared the highest nucleotide (80.9%, 81.6%, 80.5% and 80%) and amino acid (95.6%, 95.8%, 96.2% and 95.6%) identities to the CVB1 M16560, pmMC, Tucson B1 and CVB1Nm strain, respectively. Phylogenetic tree analysis showed that the MSH/KM9/2009, CVB1 M16560, pmMC, Tucson B1 and CVB1Nm strain clustered into same group. The newly isolated CVB1 strain MSH/KM9/2009 from Yunnan Province belonged to genotype CVB1.
Subject(s)
Child, Preschool , Female , Humans , Infant , Male , Base Sequence , China , Coxsackievirus Infections , Virology , Enterovirus , Classification , Genetics , Genome, Viral , Genotype , Open Reading Frames , Phylogeny , Viral Proteins , GeneticsABSTRACT
<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
The complete nucleotide sequence of two human enterovirus 71 strains (KMM09 and KM186-09) isolated in Yunnan,China, were determined by RT-PCR and sequencing. As with other human enteroviruses, the genomes were 7 409 nucleotides (nts) in length and encoded 2 193 aa. Phylogenetic analysis based on VP1 regions revealed that the two isolates belonged to subgenotype C4a. In structural genomic regions, subgenotype C4 was most homologous to other strains of C genotype when compared to other genotypes. In non-structural genomic regions, subgenotype C4 was more homologous to CA16/G10 and other strains of B genotype than to other strains of C genotype. RDP3 and Blast analysis displayed evidence of recombination in non-structural genomic regions between subgenotype B3 and C4, C4 and CA16/G10. The full-length genome of the human enterovirus 71 strains provided an overview of the diversity of genetic characteristics of a circulatinghuman enterovirus 71.