Six pools of sequence data were downloaded from GenBank: Nosema ceranae (draft genome), Spiroplasma (S. citri draft genome and all sequences longer that 500 nt), DNA viruses of arthropods (all complete genomes), all small RNA viruses of arthropods except dicistroviridae and iflavirus (complete genomes), all members of dicistroviridae and iflavirus except those infecting honey-bees (complete genomes), and all known honey bee RNA viruses (complete genomes). Each pool was converted into a Blast library and queried against the entire Solexa dataset by BlastN and tBlastx. Hits with an e-value greater than 1610 23 were extracted along with their paired end, regardless of similarity. Each pool was assembled using the Geneious sequence analysis package [102] . Contigs greater than 250 nt were queried again against the dataset by tBlastx with an e-value threshold of 1610 25 . Any positive hits were then queried against the NR database with the same parameters to eliminate spurious hits.