"Self" versus "other" delineations in biology are fascinating, from both a biological and conceptual standpoint. The example that probably leaps first into people's minds is the human microbiome: the more that is discovered about important microbes living on and in us, the more the concepts of "me"/"my"/"mine" (e.g., my body, my genome, my behavior) become hazier (a sort of metaphysical Dunning-Kruger effect?).
Is physical proximity enough to designate a microbe as part of its host's "self"? Must that association be over long periods of time? Or must it be genetic incorporation? Does a microbe only count as part of the "self" if it has some active influence on the host's life cycle? Is merely hanging out around the host enough?
The more I've learned about viruses the past handful of months, the more they've become interesting in this respect. They often stick close to their hosts, either genetically or physically, thereby enabling carryover across the lifespans of generations of hosts. Some are embedded within the human genome. Of these, some are harmless, defanged by the passage of time, like the endogenous retroviruses that comprise 1-8% of the human genome or the ribozymes related to the Hepatitis D virus. Others are more insidious, like herpesviruses that insert themselves into human telomeres. Bacteriophages regulate the bacterial inhabitants of our guts; some have, in fact, evolved hypervariable tail fibers that allow them to stick to mucins, the glycoproteins within the mucus that enswathes the GI tract.
Here's another strategy: infect gametes. Phaeoviruses do exactly that. These giant marine viruses ensure their propagation by selectively infecting the gametes of marine brown algae. One of the better studied examples is Ectocarpus siliculosus virus-1, which is able to infect both the zoospores required for asexual reproduction and the gametes required for sexual reproduction, but is only able to multiply in the algal reproductive organs. Once the viral DNA integrates into the genome, it will be propagated vertically throughout subsequent algal lineages. Clever.
Giant viruses including phaeovirus seem to share a particular penchant for infecting aquatic protists, whether that is brown algae or amoebas or phytoplankton. The first mimivirus, for example, was discovered in an amoeba growing in the water of a cooling tower in England, megavirus was found in a seawater sample in Chile, and the first pandoraviruses were isolated from Chilean seawater (again) and from an Australian pond. They are all hefty little things. The icosahedral phaeovirus capsid is about 150 nm in diameter and encloses a circular 335 kb dsDNA genome. Compare this to mimivirus with its 1.18 Mb genome in a 400 nm diameter capsid, megavirus with its 1.26 Mb genome in a 440 nm diameter capsid, or the giant pandoravirus with its 2.5 Mb genome in a 1000 nm diameter capsid. They are a dime a dozen in the open sea. If a milliliter of seawater has somewhere in the vicinity of ten million viral particles, 104 - 106 of those are giant viruses, second only in abundance to bacteriophages. What is it about the marine environment that is so amenable for giant viruses? Is there more to it than the simple physical reality of such large particles being unlikely to be dispersed through air? Does that sound like a Talmudic Question?