Host RNAs, including transposons, are encapsidated by a eukaryotic single-stranded RNA virus

Next-generation sequencing is a valuable tool in our growing understanding of the genetic diversity of viral populations. Using this technology, we have investigated the RNA content of a purified non-enveloped ssRNA virus, Flock House Virus (FHV). We have also investigated the RNA content of virus-like-particles (VLPs) of FHV and the related Nudaurelia capensis omega Virus (N?V). VLPs predominantly package ribosomal RNA and transcripts of their baculoviral expression vectors. In addition, we find that 5.3 % of the packaged RNAs are transposable elements derived from the Sf21 genome. This may be important when considering the therapeutic use of VLPs. We find that authentic FHV virions also package a variety of host RNAs, accounting for 1 % of the packaged nucleic acid. Significant quantities of host messenger RNAs, ribosomal RNA, non-coding RNAs and transposable elements are readily detected. The packaging of these host RNAs elicits the possibility of horizontal gene transfer between eukaryotic hosts that share a viral pathogen. We conclude that the genetic content of non-enveloped RNA viruses is variable, not just by genome mutation, but also in the diversity of RNA transcripts that are packaged.