**4. Materials and Methods**

#### *4.1. Sample Collection*

For vial genomic sequencing, *A. cerana* and *A. mellifera* were collected from two apiaries located in Taipei City and Yilan City, respectively, in 2018 (Figure 4; Supplementary Table S1). Besides, 3 samples of *A. mellifera* and 4 samples of *A. cerana* were selected for the investigation of variations in VP1 region (Figure 4; Supplementary Table S1). The midguts of 10 randomly selected adult bees were collected as a single sample in each apiary. The collected samples were preserved in 0.5 mL of RNA KeeperTM Tissue Sample Storage Reagent (Protech, Taipei, Taiwan) in a 1.5 mL microtube and stored at −20 ◦C for the following experiment of RNA extraction.

**Figure 4.** Locations of sample collection and the electrophoretic screening of SBV infection-positive samples by RT-PCR with primer set of VP1-F/VP1-R (Supplementary Table S2). The two sample sites for genomic sequencing were located at northern Taiwan; the AcSBV and AmSBV samples were collected in Taipei City and Yilan City, respectively. The black triangle represents the sampling site for detection of partial VP1 region (335 bp) variations in AcSBV and AmSBV in Taiwan. bp = base pair; NC = negative control. The black arrow indicated the signals of SBV positive.
