Genomic characteristics of an echovirus 20 strain (KM/EV20/2010) isolated in Kunming, Yunnan, China / 中华流行病学杂志

ABSTRACT

<p><b>OBJECTIVE</b>To identify the complete genome sequence of an echovirus 20 isolate (KM/EV20/2010) and understand its genetic variation and evolution characteristics.</p><p><b>METHODS</b>Seven 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 aligned with other echovirus 20 isolates. Phylogenetic and pairwise alignment analyses based on genome and complete VP1 regions were conducted with software Mega 4.1, RDP3 and SimPlot 3.5.1.</p><p><b>RESULTS</b>The genome of the echovirus strain was 7 395 nucleotides in length, and contained a 744-nt non-translated region (NTR) at the 5' end and a 96-nt 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. Based on the complete genome sequence alignments, the echovirus strain showed 80.1% nucleotide and 96.7% amino acid homology to echovirus 20 prototype JV-1 strain. The phylogenetic trees constructed on the genome and complete VP1 regions all indicated that the echovirus strain was not in one cluster with echovirus 20 prototype JV-1 strain, while had a closer relationship with echovirus 30 prototype Bastianni. Genotyping results from phylogenetic analysis showed that echovirus 20 has six genotypes. The strain used in this study belonged to genotype IV. The nucleotide divergence was 9.4%-21.7% among the 6 genotypes. The possible putative recombination was detected in its non-coding sequence of the echovirus 20 strain used in this study.</p><p><b>CONCLUSION</b>Based on the bioinformatics analysis. The echovirus 20 strains isolated in China could be divided into six genotypes, and the echovirus 20 in this study belonged to genotype IV.</p>