Genomic characteristics of a coxsackievirus B3 strain KM06/2009 isolated in Kunming,Yunnan,Chi-na / 中华微生物学和免疫学杂志

ABSTRACT

Objective To analyze the complete genome sequence of a coxsackievirus B 3 (CVB3) strain KM06/2009 and its genetic variation , evolution and cardiovirulence .Methods Eight clones with overlapped gene fragments covering the complete viral genome ( excluding the poly-A tail) were obtained by RT-PCR and sequenced .The nucleotide ( nt ) and amino acid ( aa ) sequences of the eight clones were aligned with sequences of other known CVB 3 clinical strains .Phylogenetic and pairwise alignment analyses based on the genome and complete VP 1 regions were conducted by using Mega 4.1,RDP3 and SimPlot3.5.1 softwares.The RNA secondary structure of CVB3 stem loopⅡ (SLⅡ) was determined by using Mfold web server.Results The complete genome of CVB3 strain KM06/2009 was 7401 nt in length, consisting of 743 nt and 100 nt on 5′untranslated region (UTR) and 3′UTR,respectively.The entire open reading frame contained 6558 nt, encoding a 2185 aa polyprotein.There was no nucleotide deletion or insertion in the coding region,but some changes of amino acid were unique .KM06/2009 strain showed 81.4%and 95.7%identities in nucleotide and amino acid sequences respectively as compared with CVB 3 prototype Nancy strain.It shared 88.4%-98.1%nucleotide and 98.1%-99.4%amino acid homology with the other Chinese clinical strains isolated at the same period .KM06/2009 strain and CVB3 GA strain without cardiovirulence shared 80.7%homology in nucleotide and 96.4% in amino acid.The phylogenetic analysis indicated that the significant spatial and temporal clustering was detected in CVB 3 isolate.CVB3 KM06/2009 strain showed a strong cardiovirulence tendency as indicated by the RNA secondary structure of CVB 3 SL Ⅱ. Conclusion CVB3 KM06/2009 isolate showed a strong cardiovirulence tendency in comparison with other CVB3 clinical isolates based on the bioinformatics analysis .