Sacbrood virus (SBV) and deformed wing virus (DWV) are evolutionarily related positive-strand RNA viruses, members of the Iflavirus group, which infect the honeybee Apis mellifera, but have strikingly different levels of virulence when transmitted orally. Honeybee larvae orally infected with SBV usually accumulate high levels of the virus, which halts larval development and causes insect death. In contrast, oral DWV infection at the larval stage usually causes asymptomatic infection with low levels of the virus, although high doses of ingested DWV could lead to DWV replicating to high levels. We investigated effects of DWV and SBV infection on the transcriptome of honeybee larvae and pupae using global RNA-Seq and real-time PCR analysis. This showed that high levels of SBV replication resulted in down-regulation of the genes involved in cuticle and muscle development, together with changes in expression of putative immune-related genes. In particular, honeybee larvae with high levels of SBV replication, with and without high levels of DWV replication, showed concerted up-regulated expression of antimicrobial peptides (AMPs), and down-regulated expression of the prophenoloxidase activating enzyme (PPAE) together with up-regulation of the expression of a putative serpin, which could lead to the suppression of the melanisation pathway. The effects of high SBV levels on expression of these immune genes were unlikely to be a consequence of SBV-induced developmental changes, because similar effects were observed in the honeybee pupae infected by injection. We suggest that the effects of SBV infection on the honeybee immunity could be an adaptation to horizontal transmission of the virus. Up-regulation of the expression of AMP genes in the SBV-infected brood may contribute to protection of the SBV virus particles in dead larvae from bacterial degradation. Suppression of the melanisation may also reduce the loss of infectivity of SBV in the larvae. Therefore it is possible that activation of AMP expression and suppression of melanisation could increase ability of SBV to be transmitted horizontally via cannibalization route. We observed no changes of AMPs and the melanisation pathway genes expression in the orally infected larvae with high levels of DWV replication alone. In the injected pupae, high levels of DWV alone did not alter expression of the tested melanisation pathway genes, but resulted in up-regulation of the AMPs, which could be contributed to the effect of DWV on the regulation of AMP expression in response to wounding. We suggest that the effects of single DWV infection on the expression of these immune-related genes could reflect evolutionary adaptations of DWV to vertical transmission. Up-regulation of AMPs is costly and suppression of melanisation may increase susceptibility to infections, therefore these changes may have negative impact on honeybee survival and, consequently, of the survival of DWV.