As you probably know, all viruses ever discovered lack the ability to replicate by themselves, and can only do so by infecting a host cell, and co-opting the molecular machinery of the cell to turn its genes into proteins, enzymes, and more genes.

I used to wonder where viruses came from, and whether it was possible that they belong to the same clade as all living organisms. I wondered if viruses could be a form of proto-life. In reality, viruses probably originated from within "living things" that already existed, and only later broke away to become rogue elements.

The genomes of most (all?) living things contain certain sequences called transposable elements, aka transposons . These sequences, though part of an organism's genome, can move around, and relocate. A large amount of an organism's genome is often in the form of transposons. Some researchers have suggested transposons as the origin of viruses. This is especially likely in the plant kingdom - angiosperms are often infected by a pathogen called a " viroid ," which is similar to an RNA virus. Researchers believe that viroids come from rogue retrotransposons .

Furthermore, there is a gene in some clades of animals that hints at the relationship between viruses and living organisms. The ARC gene seems to be essential to brain function in vertebrates, because it regulates several aspects of synaptic plasticity. The ARC gene is not an ordinary gene , however. For one thing , its transcribed RNA can jump out of its place in the genome, build a protein capsule, leave its own cell, and enter a nearby cell to be translated. Very virus-like behaviour! And obviously this gene is useful: It helps the brain coordinate over long distances, because it's mobile. But it wasn't inherited into our lineage. The leading hypothesis is that this gene is left over from a viral infection of vertebrates some time in animals' evolutionary past. Insects have a copy of this gene, too, but we think they got theirs independently , and those two lineages of slightly-different ARC gene have been evolving separately ever since. This is related to the fact that retroviruses can change the DNA of the organisms they infect. Lineages of organisms with viral DNA can even begin to produce the viruses endogenously . This means there is a strong history of co-evolution on a molecular level between viruses and living organisms.

Also, one last thing. There are these viruses called giant viruses , who belong to a group called " nucleocytoviricota ," and can reproduce using the host cell's nucleus, but can ALSO reproduce using the host cell's cytoplasm (which is full of molecular machines used to turn every type of DNA and RNA into every other type). Giant viruses can be larger than the cells they want to infect, so they can eat the cell instead, and take its cytoplasm for their replication. These viruses are so large, that they often get invaded by OTHER viruses.