The complete genome analysis of two enterovirus 96 strains isolated in China in 2005 and 2009

Enterovirus 96 (EV96) is a new member of species Human Enterovirus C (HEV-C). In this report, genomic characterization of two EV96 strains isolated from acute flaccid paralysis surveillance in Shandong province of China in 2005 and 2009 is described. The two strains, designated 05517 and 09228C1, had 82.7% genomic similarity with each other and 75.1–84.2% with other three strains available from GenBank in complete genome sequences. In VP1 coding region, they had 77.6–86.6% nucleotide similarity with other EV96 strains. Interestingly, deletions of 3 nucleotides in the VP3 coding region of strain 09228C1, and of 3 nucleotides in the 3A region of both Shandong strains were observed. Simplot and bootscanning analysis on HEV-C genome sequences were performed, and evidence of recombination in P3 region for Shandong EV96 strains was found. In conclusion, these strains had distant genetic relationship with each other and with other EV96 strains.