Phylogenetic Characterizations of Highly Mutated EV-B106 Recombinants Showing Extensive Genetic Exchanges with Other EV-B in Xinjiang, China

Abstract

Human enterovirus B106 (EV-B106) is a new member of the enterovirus B species. To date, only three nucleotide sequences of EV-B106 have been published, and only one full-length genome sequence (the Yunnan strain 148/YN/CHN/12) is available in the GenBank database. In this study, we conducted phylogenetic characterisation of four EV-B106 strains isolated in Xinjiang, China. Pairwise comparisons of the nucleotide sequences and the deduced amino acid sequences revealed that the four Xinjiang EV-B106 strains had only 80.5-80.8% nucleotide identity and 95.4-97.3% amino acid identity with the Yunnan EV-B106 strain, indicating high mutagenicity. Similarity plots and bootscanning analyses revealed that frequent intertypic recombination occurred in all four Xinjiang EV-B106 strains in the non-structural region. These four strains may share a donor sequence with the EV-B85 strain, which circulated in Xinjiang in 2011, indicating extensive genetic exchanges between these strains. All Xinjiang EV-B106 strains were temperature-sensitive. An antibody seroprevalence study against EV-B106 in two Xinjiang prefectures also showed low titres of neutralizing antibodies, suggesting limited exposure and transmission in the population. This study contributes the whole genome sequences of EV-B106 to the GenBank database and provides valuable information regarding the molecular epidemiology of EV-B106 in China.

Figure 1. Phylogenetic relationships based on the partial VP1 region sequences of EV-B106.

Four Xinjiang EV-B106 strains described in this study (indicated by circles) and other EV-B106 strains (available in the GenBank database) were analysed from the 303 nucleotides (nucleotide 2585–2887) in the partial VP1 coding region sequence. The Pakistan strain is indicated with a triangle.

Figure 2. Phylogenetic relationships based on the VP1, P1, P2, and P3 region sequences of EV-B.

Four Xinjiang EV-B106 strains (indicated by circles) and 56 other EV-B prototype strains were analysed by nucleotide sequence alignment using the neighbour-joining algorithms implemented in the MEGA 5.0 program. Numbers at the nodes indicate bootstrap support for that node (percentage of 1000 bootstrap replicates). The triangle and square indicates the Pakistan EV-B106 strain and Yunnan EV-B106, respectively. The scale bars represent the genetic distance. All panels have the same scale. (a) VP1 coding sequences; (b) P1 coding sequences; (c) P2 coding sequences; and (d) P3 coding sequences.

Figure 3. Similarity plots and bootscanning analyses of the whole genomes of Xinjiang EV-B106 strains.

(a), (c), (e), (g) Similarity plots and (b), (d), (f), (h) bootscanning analyses. A sliding window of 200 nucleotides was used, moving in 20-nucleotide steps. The four Xinjiang strains were used as query sequences independently (indicated in the upper right corner of the image).

Figure 4. Recombination analyses of the four Xinjiang EV-B106 strains with Xinjiang EV-B85 strain HYTY-ARL-AFP02F.

(a), (c), (e), (g) Similarity plots and (b), (d), (f), (h) bootscanning analyses. A sliding window of 200 nucleotides was used, moving in 20-nucleotide steps. The Xinjiang EV-B85 strain HYTY-ARL-AFP02F was used as a query sequence (indicated in the upper right corner of the image).

Figure 5. Temperature sensitivity test curves of the four Xinjiang EV-B106 isolates.

A Xinjiang EV-B85 strain (strain HYTY-ARL-AFP02F, showing non-temperature sensitivity) was used as an experiment control. The blue and red lines represent the growth trend of the viruses on RD cells at 36 °C and 39.5 °C, respectively. (a) strain HTPS-QDH11F (EV-B106); (b) strain KS-KSH28F/XJ (EV-B106); (c) strain KS-MGTH90F (EV-B106); (d) strain AKS-AWT-AFP2F (EV-B106); (e) strain HYTY-ARL-AFP02F (EV-B85).