Contigs that appeared divergent or that were derived from nonhoney bee associated viruses were extended using the entire read dataset using a paired-end contig extension algorithm (''PRICE'' Graham Ruby, manuscript under preparation, software available at http://derisilab.ucsf.edu). The extended contigs were then independently confirmed by PCR recovery and Sanger sequencing. Individual paired-end reads that were discordant with the recovered contigs were used to further nucleate new contigs via contig extension. Primer3 [103] was used to design primers bridging adjacent contigs, as determined by mapping onto known virus genomes. Individual viruses or other microbes were queried with a BlastN threshold e-value of 1610 27 (W7) to determine read counts.