Table 1 shows the pairwise aa (polyprotein, 2C + 3CD, P1-P3, VP1-VP4 and 3D) or nt (5′UTR and 3′UTR) identity of BEV-AN12 to representative strains of each species belonging to BEVs and other Japanese BEVs. Deduced aa sequences encoding polyprotein, 2C + 3CD, P1, P2, P3, 3D and four capsid proteins (encoding VP4, VP2, VP3 and VP1) were compared to each EV-E and F. BEV-AN12 possessed showed identity to EV-Fs in polyprotein, 2C + 3CD, P2, P3 and 3D than to those of EV-Es. However, low aa identity (aa identity <70%) was observed in P1 to EV-Es and EV-Fs. Particularly, the VP1 region of BEV-AN12 encoded in P1 showed a significantly low aa identity to other BEVs (54.7% ≤ aa identity ≤ 58.6%). As a result of multiple alignment analysis, several motifs conserved among the genomes of genus Enterovirus were detected in the genome of BEV-AN12. In particular, the [PS] ALXAAXETG motif in VP1, GXCG motif in 2A, GXXGXGKS motif for NTP-binding in 2C, GXCG motif forming part of the catalytic active site in 3C, and KDE [LI] R in 3D were identified [47–50]. However, the putative cleavage site at the junction of VP3/VP1 was a glutamine/serine for BEV-AN12. In addition, a 6-aa insertion in the 2A region was identified at position 835–840 aa (PLRTTG) in the BEV-AN12 genome. Multiple alignment using aa sequences encoding polyprotein is supplemented as Additional file 2: Table S2.Table 1Pairwise nucleotide (5′UTR and 3′UTR) and amino acid (polyprotein, 2C + 3CD, P1-P3, 3D and VP1-4) identity (%) of BEV-AN12 to Japanese BEVs, EV-Es and EV-FsBEV AN12/Bos Taurus/JPN/2014 (LC038188)Bovine enterovirus in JapanEV-E1EV-E2EV-E3EV-E4EV-F1EV-F2EV-F3EV-F4IS1/Bos taurus/JPN/1990(LC150009)IS2/Bos taurus/JPN/1990(LC150010)Ho12/Bos taurus/JPN/2009 (﻿LC150008)LC-R4 (DQ092769)K2577 (AF123432)HY12 (KF748290)PAK-NIH-21E5 (AFK92921)BEV-261 (NC_021220)3A (AY508697)PS87/Belfast (DQ092794)Possum enterovirus W6 (AY462107)5′UTR76.179.880.875.874.271.1N/A81.880.481.378.0Polyprotein73.686.686.273.273.672.7N/A85.084.685.682.42C + 3CD80.998.898.680.780.980.2N/A98.198.193.697.9P165.868.768.365.166.064.5N/A68.267.267.667.1VP475.485.585.575.479.775.4N/A82.685.585.582.6VP274.272.673.072.272.673.4N/A72.671.471.070.2VP365.071.671.265.865.864.6N/A70.070.070.872.8VP156.957.956.854.756.556.254.756.158.655.056.8P277.896.495.778.077.677.3N/A92.391.694.989.7P379.098.898.578.679.178.3N/A98.098.398.393.73D84.099.198.783.783.783.5N/A98.798.998.995.03′UTR71.686.1N/A71.671.673.0N/A84.786.186.181.9N/A: Sequences are not available