After gaining entry into the cell (understanding the mechanics of which requires a PhD unto itself..), viral proteins translate the viral genome into a language that can be read by the ribosome. Expression of host genes is suspended, and the entire cell becomes a factory for producing more viruses. Once the program is fulfilled, the cell lyses, and the newly minted viruses go on to repeat the process.

This behavior is what leads to the debate about whether or not viruses are alive. They fulfill some basic functions of life, but they always need a host cell that allows them to do so. There are other parasitic organisms that require a host to complete their life cycle, but none that have as few essential functions as viruses. There’s even a strange cnidarian parasite of salmon which is the only animal discovered to date that doesn’t need oxygen to breathe - but without a breathing apparatus, it still codes for far more functions than a virus does.

What are all these viruses doing?

The world we live in is covered in viruses. They’re so numerous in seawater that one paper referred to the ocean as “virus soup,” which in addition to being disgusting, raises the question - what are they doing?

The most obvious answer is that they’re providing a vast quantity of nutrients for the bottom of the food chain in every ecosystem on earth. When they attack and destroy their host cells, the contents of the targeted cells spill out into the environment. The kind of nutrient content their activity provides is, by definition, formative for the biological abundance.

In addition to nutrient content, all that unique genetic information we talked about earlier also comes in handy. The sheer amount of viruses present in the environment, and the sheer amount of genetic diversity in them, means that viruses contain the greatest reservoir of genetic information in the world. People frequently wonder where new genes come from - and the answer is they most likely come from viruses.

This sort of genetic exchange has already been recorded. Some strains of E. coli contain enormous sections in their genomes that came directly from viruses. These so-called “prophages” account for 16% of some E. Coli DNA sequences. The integrated viral DNA has various functions. Some excerpts from Start-up entities in the origin of new genes

… in Pseudomonas aeruginosa, genes encoding the tail of two different bacteriophages have been converted into bacteriocins used by the bacteria to kill its competitors

In eukaryotes, it also seems that transposable elements have served as substrates for new genes: in Drosophila, the extension of chromosome ends involves proteins similar to those encoded by two long interdispersed element (LINE)-like retrotransposons, TART (telomere-associated retrotransposon) and HeT-A, suggesting that, in the fly lineage, genes from transposable elements have assumed the function usually achieved by telomerases

Recently, Mallet et al. have reported that a gene from a human endogenous retrovirus, which is restricted to the hominoid lineage has taken on an active role in formation of the human placenta, possibly by favoring cell fusion

Where did they come from?

It is apparent that viruses play an instrumental role in biology, but it’s less clear where they came from. There are three different opinions, which can be classified as:

Virus first

Reductive virus

Escaped genes

Virus first suggests that viruses were here before any other kind of life, that they arrived on a barren but chemically rich planet. It doesn’t really account for the fact that viruses need someone else’s workbench in order to make more of themselves. Given their tendency to fall apart when outside of cells for too long, there’s too many different things that aren’t likely..

The reductive virus theory suggests that viruses were more complex organisms that were whittled down over time to just be these informational packets.

Escaped genes suggests that the genetic contents of viruses are “self aware” entities that escaped from known organisms in order to make a go of it themselves.

Proponents of this theory consider viruses to be inevitable outcomes of a genetic system - parasites that arise to take advantage of machinery without having to pay the cost of producing it. And the reason that they’re still around is because “the unescapable cost of maintaining sufficiently powerful defense systems.”

Others simply sidestep the question of where they came from and if they’re alive or not, and call them an illustration of the replicator paradigm - a paradigm that contains the whole collection of self-replicating oddities found in cells. Transposons, plasmids, even chromosomes and organelles all copy themselves and move between cells. Sure, we make a distinction that their movement is part of a “normal” process - but, perhaps, so is viral movement.

None of these theories, though, account for the astounding genetic diversity of viruses. If viruses originate from the cells that they interact with, one would expect there to be significant genetic overlap between the host and the parasite. However, that just simply isn’t the case. Viruses show almost the exact opposite - as far as we can tell, there’s no end to their diversity. It’s almost like new ones are being added as quickly as old ones degrade and disappear.

Okay Doc, Be Straight With Me. Are Viruses From Outer Space?

We’re almost there, hang in there. A brief recap of what has been shown about viruses:

There’s a seeming endless supply of them

They outnumber all other life forms on earth

They’re entirely dissimilar from each other

They’re entirely dissimilar from all other forms of life

No genetic sequence appears in all viruses

Bacterial and human DNA contains large sections of inactivated viral DNA

Bacteria re-appropriate viral genes for other necessary functions

All of these facts together suggest that viruses are the raw material from which living creatures build their genetic material. They’re like bricks in a building, and cellular processes the mortar that holds it all together. If that’s the case, you’d expect to end up with enormous viruses, ones that rival the structural complexity of the simplest bacteria…

And, in fact, that’s exactly what you see - viruses like the Pandoravius, and the megaviridae, and tupanvirus have enormous genomes, rivaling the complexity of their bacterial counterparts. The only pieces they’re still missing before they get classified along with the rest of the bacterial oddities on the tree of life? The ability to produce their own proteins. Once they acquire the software necessary for that, or accidentally envelop a compatible ribosomal protein factory, the transition would happen spontaneously.