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The human gut has an indispensably beneficial ecosystem of bacteria. What are the examples of a virus that becomes symbiotic with an organism, or even incorporates beneficially into the genome of the organism?

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In humans, endogenous retroviruses (HERVs) comprise a substantial fraction of the genome, as much as 8%. While many historical viral incorporation events into the primate genome were likely neutral or detrimental (and therefore selected against), some were co-opted and are now functional elements in humans. An example: human syncytin is the envelope gene of a defective HERV, and the protein has been co-opted for fusion during human placentation. More HERV resources here. The Feschotte Lab at Cornell studies the evolution of HERVs and other mobile elements in mammalian genomes, and their lab site provides more resources.

In bacteria, prophage (integrated bacteriophage) can be co-opted by their hosts for niche-specific transcriptional control. A cool example is the pathogen Listeria monocytogenes, which utilizes prophage excision during intracellular growth to activate its Com system and escape from phagosomes.

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In certain species of parasitic wasp, contained within the wasp genome is the genome for a so-called "polydnavirus". The female wasp somehow creates instances of these polydnaviruses inside its ovaries.

When the wasp injects an egg into a member of the host species (likely a caterpillar), several instances of the polydnavirus are also injected along with it. Although the viruses do not harm the wasp in any way, they do have an immunosuppressant effect on the caterpillar, protecting the wasp egg against the caterpillar's immune system.

I've seen an article in "The Atlantic" which claims the viruses can also manipulate the caterpillar's metabolism in a way beneficial to the parasitic larva, but the article did not provide a source for this.

The polydnaviruses, counterintuitively, cannot actually replicate themselves, and are only "reproduced" when the wasp's cells manufacture them! They do not reproduce inside the caterpillar, serving only to protect the wasp egg/larva and copies of the virus genome encoded in the larva's DNA.

(Actually, for some wasp-species/virus pairings, the viruses may exist and reproduce inside the wasp ovaries instead of being "manufactured" by the wasp.)

If you found this interesting, you may also want to look up "virus-like particles", which are created and used by the wasp in the same way, but do not contain any nucleic acid. Regrettably, I don't know enough about these to elaborate further.

So there you have it! A virus which is very beneficial to its wasp host - or at least to that host's offspring - although certainly not to its later caterpillar host.

Sources:

See also:

https://www.theatlantic.com/science/archive/2015/09/parasitic-wasps-genetically-engineer-caterpillars-domesticated-viruses/405874/

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