**Table 4.** Amino acid sequence homology (%) of AcSBV-TW, AmSBV-TW, and 54 other SBV

 strains.

 94

 95

 93

 93

 95

 96

 99

 100

 96

 75

 96

 96

*Pathogens* **2021**, *10*, 14

**Table 4.** *Cont.*



Comparisons of nucleotide and amino acid sequences revealed the deletion of 51 base pairs (17 amino acids) in AcSBV-TW (from amino acid positions 712–730 (VP1 region) in the ORF region) compared to AmSBV-TW, and the same deletion (AC-genotype) was found in most of the other SBVs from *A. cerana*, including AcSBV-Viet1, 2, 3, 5, AcSBV-Hynor, AmCSBV-SDLY, CSBV-JLCBS-2014, AcSBV-Korean, AcSBV-Kor3, 4, AcSBV-Viet-NA, AcSBV-Viet-BG, except AmSBV-Kor19 and AmSBV-Viet4 (Figure 2). Another 10–13-aminoacid deletion was found in six SBVs from *A. cerana* in India and two SBVs from *A. cerana* in China, including AcSBV-India-II2, -II9, -II10, -K1A, -K5B, -TN-1, CSBV-LNQY-2009, and CSBV-FZ (Figure 2). However, a less than 10-amino-acid deletion was found in the SBVs from *A. mellifera* in Australia, including AmSBV-VN3 and SA (Figure 2). Similar to other SBVs from *A. mellifera,* AmSBV-TW showed no deletion in the 712–730 amino acid region of the ORF (AM-genotype), and same to the AcSBVs from China (CSBV-GZ, -BJ, -SXnor1, and SXYL-2015), India (AcSBV-India-K3A and -S2), and Vietnam (AcSBV-Viet-BP, -LDst, and -SBM2) also lacked the 17-amino-acid deletion (Figure 2).

**Figure 2.** Phylogenetic tree constructed based on the polyprotein amino acid sequences of AmSBV-TW and AcSBV-TW and 54 other SBV strains from the NCBI database. The phylogenetic tree was constructed using the neighbor-joining (NJ) method and 1000 bootstrap replications. The pairwise alignment indicated the deletion patterns in the VP1 region of SBV strains. The round shape symbols indicated AmSBVs with AC genotype (deletion in VP1 region), and the red triangle shape symbols indicated AcSBVs with AM genotype (non-deletion in the VP1 region). red font: The Taiwan strains from this study. \*: A note for every 10 bases.
