After reading about so-called "mystery proteins" in this excellent summary of the coronavirus genome (and acknowledging that the "mystery" simply reflects our lack of knowledge about a very new virus), I'm curious if any known viruses can contain parasitic genetic information "along for the ride", or if their genomes are selected, generally speaking, to be as informationally efficient as possible, for what is encoded? In other words, does selection pressure allow for these parasites to contain their own parasites, and are there known examples of such, if so?
I'm curious if any known viruses can contain parasitic genetic information "along for the ride"
Analogous to the parasitic transposons mentioned in the paper linked by canadianer, phage-inducible chromosomal islands are mobile elements that "hijack" the molecular machinery of bacteriophage during lytic infection of Gram-negative hosts. PICI elements, as they're called, encode Rpp proteins that complex with the phage TerS homodimer, changing the conformation of the complex such that the PICI cos mimic is preferentially bound and packaged into the empty capsid. Fillol-Salom et al. 2019 1 discuss in detail the mechanism of PICI propagation and provide a good graphical abstract of the process:
Similar elements exist in Gram-positive bacteria, specifically Staphylococcus aureus, called Staphylococcus aureus pathogenicity islands (SaPIs). Instead of encoding a separate protein that complexes with the phage TerS, SaPIs encode a homolog of TerS that specifically recognizes and packages SaPI DNA into phage capsids.2
Note that this answer does not directly address the question of "junk" DNA in viruses, as PICI elements are dormant in the genomes of the bacterial hosts rather than the genomes of the viruses themselves. Though, I believe this is relevant insomuch that they parasitize bacteriophage, and are therefore "along for the ride" in the viral capsid.