Complete genome characterization of a novel enterovirus type EV-B106 isolated in China, 2012

Abstract

Human enterovirus B106 (EV-B106) is a recently identified member of enterovirus species B. In this study, we report the complete genomic characterization of an EV-B106 strain (148/YN/CHN/12) isolated from an acute flaccid paralysis patient in Yunnan Province, China. The new strain had 79.2-81.3% nucleotide and 89.1-94.8% amino acid similarity in the VP1 region with the other two EV-B106 strains from Bolivia and Pakistan. When compared with other EV serotypes, it had the highest (73.3%) VP1 nucleotide similarity with the EV-B77 prototype strain CF496-99. However, when aligned with all EV-B106 and EV-B77 sequences available from the GenBank database, two major frame shifts were observed in the VP1 coding region, which resulted in substantial (20.5%) VP1 amino acid divergence between the two serotypes. Phylogenetic analysis and similarity plot analysis revealed multiple recombination events in the genome of this strain. This is the first report of the complete genome of EV-B106.

Figure 1. Nucleotide insertions and deletions and the resulted amino acid changes in the P1 region among EV-B106 strains (a) and with EV-B77 strains (b).

Nucleotide positions are numbered according to strain 148/YN/CHN/12 (a) and EV-B77 prototype strain CF496-99 (b). The red and blue squares indicate the nucleotide frame shifts and associated amino acid changes, respectively.

Figure 2. Phylogenetic relationships of the EV-B106 strains and other EV-B prototype strains.

The phylogenetic trees based on nucleotide sequences for P1 (a), P2 (b), and P3 (c) coding regions were constructed from the nucleotide sequence alignment using the neighbor-joining algorithm of the MEGA 4.0 software.

Figure 3. Similarity plot (a) and bootscanning analysis (b) of Yunnan EV-B106 strain with EV-B prototype strains.

The analysis was conducted via Simplot v3.5.1 using a sliding window of 400 nucleotides moving in steps of 20 nucleotides. The genome of strain 148/YN/CHN/12 serves as a query sequence. One possible recombination event between 12148/YN and EV-B107 is suggested in the 2B region (about nt positions 3700–3960).

Figure 4. Similarity plot (a) and bootscanning analysis (b) of the Yunnan EV-B106 strain with closely related strains.

The analysis was conducted via Simplot v3.5.1 using a sliding window of 400 nucleotides moving in steps of 20 nucleotides. The genome of strain 148/YN/CHN/12 serves as a query sequence. Several possible recombination events are suggested in P2 and P3 coding regions.