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DWV was the most common virus in A. mellifera, and its infection rate and load in A. mellifera were higher than those in A. cerana, which reflects the high susceptibility of A. mellifera to Varroa destructor infestation. The infection rate and viral load of SBV were higher in A. cerana than in A. mellifera, indicating that SBV poses a greater threat to A. cerana than to A. mellifera. Our results also suggested that there was no geographical variation in viral dynamics in A. mellifera and A. cerana. Phylogenetic analyses of BQCV, DWV, I