Ok, some free form conjecturing here, in case anyone is interested.
So the first fossils of eukaryotes are found at about 2.1 billion years ago. Scientists think that eukaryotes existed about 2.7 bya, but getting fossils of soft skinned single celled creatures with organelles is very rare.
PDF link
So let's say 2.7 bya, large prokaryotes get invaded by smaller prokaryotes which begin a symbiotic relationship to form the first eukaryotes. At the same time, viruses evolve that can infect these new hybrid creatures. Among these viruses are the Megaviridae or giant viruses. These viruses seem to have some metabolic independence from their victims. For the link above:
"Mimivirus genes were found to encode proteins unique amongst viruses and involved in DNA repair, protein folding, nucleotide synthesis, amino acid metabolism, protein modification, or lipid or polysaccharide metabolisms"
In our time these viruses seem only to attack the most simple of all the Eukaryotes, the unicelluler Amoebi. The modern day amoeba, while 2.7 billion years farther along, is the closest living organism to the first eukaryotes.
But the viruses that evolved to attack modern, more advanced organisms, such as Influenza, Smallpox, the common cold are much simpler in design and do not contain any of the above genes. Does this mean modern viruses (that plague humans) lost the ability to internally control their own metabolism and, instead, gained the ability to fully exploit the manufacturing processes within the target cells? In other words the more modern viruses have given up some metabolic autonomy in return for more efficiently utilizing the metabolism mechanisms of their host cells.