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Enterovirus 87 (EV87) is a new member of species Human Enterovirus B. So far, only the genome sequence of the prototype strain from Bangladesh is available. Here, we report the genome sequence of EV87 strain LY02/SD/CHN/2000 isolated from an acute flaccid paralysis case in Shandong Province, China, in 2000. It has a genome of 7423 nucleotides. Compared with the prototype strain, it had 80.3 % nucleotide and 95.5 % amino acid similarity in the VP1 coding region and 82.8 % complete genome similarity, reflecting distant genetic relationship between them. Phylogenetic analysis provided evidence of recombination with other serotypes in the P2 and P3 coding regions.

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.

Human enterovirus B73 (EV-B73) is a member of species Enterovirus B. To date, only one complete genome sequence of prototype strain CA55-1988 from California has been available. In this study, the complete genome analysis of an EV-B73 strain 088/SD/CHN/04 isolated from an acute flaccid paralysis case in Shandong Province, China in 2004 is conducted. It had 75.6 and 79.3 % nucleotide similarity with prototype strain CA55-1988 in the VP1 coding region and the complete genome, respectively. It had great VP1 nucleotide divergence (16.7–24.4 %) with EV-B73 strains from other parts of the world. Similarity plot and bootscanning analyses provided evidence of recombination with other EV-B viruses.

Echovirus 11 (E11) is an important human pathogen, but its genetic information in China is in scarce. In this study, 12 sewage samples from Jinan city and 18 from Linyi city were collected in Shandong Province, China in 2010, and E11 was the predominant serotype with 54 isolates from 16 samples. Numbers of E11 isolates reached peaks in August in both Jinan and Linyi city, while another peak occurred in December in Linyi. The complete VP1 genes of all these isolates were sequenced and phylogenetically compared with clinical isolates from Shandong in 1994–2010 (n = 29) and global E11. Shandong isolates segregated into five clusters, four in genogroup A and one in genogroup C. Environmental isolates belonged to two clusters of genogroup A, with high inter-cluster genetic divergence (18.5–20.9%). No local clinical E11 was isolated in the two cities in 2010, revealing the value of environmental surveillance in investigating circulating viruses. These findings underscored the significance of environmental VP1 sequence divergences in comprehending the local enterovirus circulation, and updated the global molecular epidemiology of E11.

The genomic characterization of human enterovirus 97 (EV97) strain isolated from an acute flaccid paralysis case in Shandong province, China in 1999, is described. The strain, designated as 99188/SD/CHN/1999/EV97 (abbreviated as 99188), had a genome of 7394 nucleotides. Compared with other EV97 strains, it had 81.3–83.3% nucleotide similarity and 94.0–95.4% amino acid similarity in VP1 coding region, and it had 81.4% complete genomic similarity with prototype strain BAN99-10355. The most striking feature was the deletion of 18 nucleotides in the 3′ end of VP1 coding region, combined with two deletions and one insertion in 5′ and 3′ untranslated regions. All these findings demonstrated the strain 99188 had a distant genetic relationship with other EV97 strains. In the phylogenetic trees generated from VP1 and 3D sequences of human enterovirus species B (HEV-B), the lineages of strain 99188 were not congruent, suggesting the event of recombination. Similarity plot analysis further provided the evidence of recombination with other strains of HEV-B in P2 and P3 coding region. This is the first finding of EV97 in China and the third genomic sequence of EV97 reported.