Typically, people call viruses some kind of organic compounds that cannot reproduce autonomously and which lower the fitness of their hosts. Even the word "virus" means "venom" in Latin.
But from the perspective of natural selection, one would expect those organic compounds that cannot reproduce autonomously, but which would increase the fitness of their hosts, to be more widespread. One can see an analogy with bacteria: people are more aware of harmful bacteria and even such words as "microbe" are perceived as somewhat harmful (among non-biologists for sure). But we know that an animal body contains many more useful bacteria than harmful ones, and animals have their own microflora, which are necessary for survival.
The same must be true for viruses: those viruses which were useful (or at least unharmful) to their hosts would be passed more easily to other organisms since their hosts would have a selective advantage.
So, do such beneficial viruses exist? If so, what are they called? What are the examples?
Do they exist? Yes
What are they called? Marilyn Roossinck calls them viral mutualistic symbiotes. She has an excellent review here.
What are some examples?
My personal favorite is GB-Virus C, or Hepatitis G, which appears to slow the progression of HIV using a number of different mechanisms:
Box 1. Summary of the effects of GBV-C infection in HIV-positive individuals
- GBV-C infection downregulates HIV entry co-receptors CCR5 and CXCR4, and increases secretion of their ligands RANTES, MIP-1α, MIP-1β and SDF-1.
- In vitro GBV-C NS5A and E2 proteins inhibit X4- and R5-tropic HIV replication, and NS5A protein downregulates CD4 and CXCR4 gene expression.
- HIV-infected individuals positive for GBV-C E2 antibodies have survival benefit over HIV-infected individuals with neither GBV-C viremia nor E2 antibodies; in vitro GBV-C E2 antibodies immunoprecipitate HIV particles and inhibit X4- and R5-tropic HIV replication.
- GBV-C induces activation of interferon-related genes and pDCs.
- GBV-C promotes Th1 polarization and the NS5A protein contributes to this effect.
- GBV-C infection reduces surface expression of activation markers on T lymphocytes, suggesting its role in T cell activation signaling pathways.
- GBV-C protects the T cell from Fas-mediated apoptosis and as a result of its effect on immune activation may also play a role in protecting lymphocytes from activation-induced cell death.
- GBV-C viremia reduces IL-2-mediated T cell proliferation suggesting a significant interaction between GBV-C, IL-2 and IL-2 signaling pathways.
As @mbrig recalls in the comments, there are a number of retroviruses that have inserted themselves into the germ line. Those are called endogenous retroviruses, and they interact with the host genome in a number of ways. Some are even translated:
Proteins produced from ERV env genes have also been demonstrated to function as restriction factors against exogenous retroviral infection
Another good virus would be a Bacteriophage, a virus that eats bacterial illness. From Wiki:
A bacteriophage also known informally as a phage, is a virus that infects and replicates within Bacteria and Archaea. The term was derived from "bacteria" and the Greek φαγεῖν (phagein), "to devour". Bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, and may have relatively simple or elaborate structures.
They have been used for over 90 years as an alternative to antibiotics in the former Soviet Union and Central Europe as well as in France. They are seen as a possible therapy against multi-drug-resistant strains of many bacteria.
Intentionally using Bacteriophages medicinally is called phage therapy.
I would say that if any "good" viruses exist, they are already within us. Retrotransposons are genetic elements in our DNA that were likely ancient viruses and they move around from time to time either by excising themselves and moving somewhere else or by making a copy and inserting it somewhere else in the genome. Even though we are born with them, their activity is similar to modern viruses. When retrotransposons insert themselves in a new place they can cause disease, but the variation they cause likely brought us some beneficial advantage at some point because we have so many of them and they stuck around this long.
Cowpox and smallpox viruses structurally similar, and catching one confers immunity to both by immune system response, but one was a deadly disease and the other almost harmless. Once this was discovered, the days of smallpox were numbered. We had the means and the motivation to stamp it out.
On my last check a few years ago, we are deliberately keeping cowpox alive to ensure that we can kill smallpox should it ever come back.
The virus that ended a plague is a good virus.
Per my comment and response:
The most current example (at this time and based on my recollection) is the virus we have engineered to treat a certain type of macro degenerative eye condition:
There are a few other cases out there, and, as always, xkcd is there to help:
Biologically, all viruses by themselves are bad. More accurately, they have a negative effect. They work by injecting a strand of DNA into one of the host's cells, which makes the cell produce viruses instead of more cells. However, some viruses negative effect when paired with another virus can produce a double negative. Unfortunately, it never quite cancels out.
To sum it up, if you have a virus, there is definitely something bad happening in your system.