Abstract
Black soldier flies (BSFs, Hermetia illucens) are becoming a prominent research model encouraged by the insect as food and feed and waste bioconversion industries. Insect mass-rearing facilities are at risk from the spread of viruses, but so far, none have been described in BSFs. To fill this knowledge gap, a bioinformatic approach was undertaken to discover viruses specifically associated with BSFs. First, BSF genomes were screened for the presence of endogenous viral elements (EVEs). This led to the discovery and mapping of seven orthologous EVEs integrated into three BSF genomes originating from five viral families. Secondly, a virus discovery pipeline was used to screen BSF transcriptomes. This led to detecting a new exogenous totivirus that we named hermetia illucens totivirus 1 (HiTV1). Phylogenetic analyses showed this virus belongs to a clade of insect-specific totiviruses and is closely related to the largest EVE located on chromosome 1 of the BSF genome. Lastly, this EVE was found to express a small transcript in some BSFs infected by HiTV1. Altogether, this data mining study showed that far from being unscathed from viruses, BSFs bear traces of past interactions with several viral families and of present interactions with the exogenous HiTV1.