Back in 2009, I wrote some Python scripts to use the NCBI Entrez Utilities to search for and download all known complete virus genomes in GenBank format, which I then processed to make FASTA files and BLAST databases. Recently I updated them and ran into some problems... false positives like entire bacterial genomes! This turns out to be due to a few bacteria with integrated phage being annotated as chimeras - genomes combined from multiple organisms.
