*Article* **Genomic Sequencing and Comparison of Sacbrood Viruses from** *Apis cerana* **and** *Apis mellifera* **in Taiwan**

**Ju-Chun Chang 1,2, Zih-Ting Chang 1, Chong-Yu Ko 1, Yue-Wen Chen 1,\* and Yu-Shin Nai 2,\***

<sup>1</sup> Department of Biotechnology and Animal Science, National Ilan University, Yilan 260, Taiwan;

c1887g@gmail.com (J.-C.C.); a0923653853@gmail.com (Z.-T.C.); ricardo7677@gmail.com (C.-Y.K.)

<sup>2</sup> Department of Entomology, National Chung-Hsing University, Taichung 402, Taiwan **\*** Correspondence: chenyw@niu.edu.tw (Y.-W.C.); ysnai@nchu.edu.tw (Y.-S.N.)

**Abstract:** Sacbrood virus (SBV) was the first identified bee virus and shown to cause serious epizootic infections in the population of *Apis cerana* in Taiwan in 2015. Herein, the whole genome sequences of SBVs in *A. cerana* and *A. mellifera* were decoded and designated AcSBV-TW and AmSBV-TW, respectively. The whole genomes of AcSBV-TW and AmSBV-TW were 8776 and 8885 bp, respectively, and shared 90% identity. Each viral genome encoded a polyprotein, which consisted of 2841 aa in AcSBV-TW and 2859 aa in AmSBV-TW, and these sequences shared 95% identity. Compared to 54 other SBVs, the structural protein and protease regions showed high variation, while the helicase was the most highly conserved region among SBVs. Moreover, a 17-amino-acid deletion was found in viral protein 1 (VP1) region of AcSBV-TW compared to AmSBV-TW. The phylogenetic analysis based on the polyprotein sequences and partial VP1 region indicated that AcSBV-TW was grouped into the SBV clade with the AC-genotype (17-aa deletion) and was closely related to AmSBV-SDLY and CSBV-FZ, while AmSBV-TW was grouped into the AM-genotype clade but branched independently from other AmSBVs, indicating that the divergent genomic characteristics of AmSBV-TW might be a consequence of geographic distance driving evolution, and AcSBV-TW was closely related to CSBV-FZ, which originated from China. This 17-amino-acid deletion could be found in either AcSBV or AmSBV in Taiwan, indicating cross-infection between the two viruses. Our data revealed geographic and host specificities between SBVs. The amino acid difference in the VP1 region might serve as a molecular marker for describing SBV cross-infection.

**Keywords:** sacbrood virus; sacbrood disease; *Apis cerana*; *Apis mellifera*
