Genomic characteristics of coxsackievirus B1 MSH/KM9/2009 strain isolated in Yunnan, China / 病毒学报

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.

Complete nucleotide sequence of a human echovirus 6 strain KM57-09 isolated in Yunnan,China,in 2009 / 中华流行病学杂志

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.