Genomic characteristics of coxsackievirus B5 A210/KM/09 strain isolated in Yunnan, China.

Jiansheng Liu; Congwen Shao; Weizhong Zhao; Yunkun Zhang; Ma JI; Yanju Zhu; Zhongfei MA; Shaohui MA

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Genomic characteristics of coxsackievirus B5 A210/KM/09 strain isolated in Yunnan, China.

Author: Jiansheng LIU ¹ ; Congwen SHAO ¹ ; Weizhong ZHAO ¹ ; Yunkun ZHANG ¹ ; Ma JI ¹ ; Yanju ZHU ¹ ; Zhongfei MA ¹ ; Shaohui MA ²
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1. Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Disease, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China.
2. Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Disease, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China. Email: shaohuima70@hotmail.com.
Publication Type:Journal Article
MeSH: Child, Preschool; China; epidemiology; Encephalitis, Viral; epidemiology; virology; Enterovirus B, Human; genetics; isolation & purification; Female; Genome, Viral; Genotype; Humans
From:Chinese Journal of Epidemiology 2014;35(3):307-311
CountryChina
Language:Chinese
Abstract:
OBJECTIVETo characterize the complete genome sequence of coxsackievirus B5 (CVB5)A210/KM/09 strain which was isolated from Yunnan, China, 2009.
METHODSEight overlapping clones covering the whole viral genome (excluding the poly-A tail)were obtained by RT-PCR and sequenced, with their nucleotide and amino acid sequences compared with other known CVB5 strains.
RESULTSThe genome of the CVB5 A210/KM/09 strain had 7 372 nucleotides in length, and containing a 742-nt non-translated region (NTR) at the 5' end and a 98-nt NTR at the 3' end. The entire open reading frame contained 6 555 nt, encoding a 2 185-aa polyprotein. In the coding region, there appeared no nucleotide deletion or insertion, but some changes of amino acid seemed unique. Based on the complete genome sequence alignments, CVB5 isolate A210/KM/09 strain showed the highest nucleotide (92.5%) and amino acid (97.3%) identities to the CVB5/CC10/10. It also shared nucleotide (80.1%-92.5%) and amino acid (95.0%-97.3%) homology with other CVB5 strains: 17Y, 19CSF, 20CSF, 1954/85/US, 2000/CSF/KOR, 03001N, CoxB5/Henan/2010, VB5/SD/09 and Faulkner. Blast between genome fragments, A210/KM/09 showed similarity on nucleotide (80.1%-92.5%) and amino acid (95.0%-97.3%) identities with other CVB5 strains. The phylogenetic tree, constructed on the complete VP1 regions, indicated that CVB5 could be divided into genotype A, B, C and D. while Genotype C and D could be further divided into C1-C4 and D1-D4 subgenotypes.
CONCLUSIONA210/KM/09 and other CVB5 predominant strains isolated in China belonged to CVB5 subgenotype C4.