Behaviour manipulation imposed by parasites is a fascinating phenomenon but our understanding is still very limited. We studied the interaction between a virus and the parasitic wasp Leptopilina boulardi that attacks Drosophila larvae. Wasps usually refrain to lay eggs into already parasitized hosts (superparasitism avoidance). On the contrary, females infected by the Leptopilina boulardi Filamentous Virus (LbFV) are much more incline to superparasitize. Interestingly, the host-sharing induced by this behaviour modification leads to the horizontal transmission of the virus, thus increasing its fitness at the expense of that of the wasp. To better understand the mechanisms underlying this behaviour manipulation, we studied by RNA sequencing the meta-transcriptome of LbFV and the parasitic wasp both in the abdomen and in the head. We found that the abundance of viral transcripts was independent of the wasp strain but strongly differed between tissues. Based on the tissue pattern of expression, we identified a set of 20 viral genes putatively involved in the manipulation process. In addition, we identified a set of wasp genes deregulated in the presence of the virus either in the abdomen or in the head, including genes with annotations suggesting involvement in behaviour (i.e. Potassium-channel protein). This dataset gives new insights into the behaviour manipulation and on the genetic basis of superparasitism in parasitoids.