The Past is Present: What Ancient Viruses Can Teach Us About Their Modern Counterparts

Although viruses are microscopic, thanks to the COVID-19 pandemic, they have never been more visible than before. And as more people seek to understand them, the more their origins are called into question.

For a long time, many scientists accepted the theory the tiny packets of genomes we call viruses, were mutated cells: cells that regressed to the point where they could not replicate on their own. Of course, several other theories came forward. One, in particular, suggests that they escaped from living cells and devolved over time, eventually becoming parasitic. To be fair, viruses do have these traits, but these traits likely came from recent rather than ancient adaptations.

In fact, evidence is piling up that ancient viruses may have been something entirely different than the viruses we see today. Researchers who have recently reconstructed viral lineages found that viruses may have emerged as molecular entities that predate the last universal cellular ancestor (the common ancestor of everything living today.)

Today, scientists class viruses as “nonliving” because they lack many characteristics necessary for life. In particular, viruses lack the ability to reproduce on their own and to metabolize food for energy. In contrast, ancient viruses, or at least some of them, may have been more complex and larger than cells.

How do what ancient viruses were like? No one has ever found a virus fossil. But luckily for scientists, they don’t need to. Like crocodiles, alligators, and komodo dragons, animals that have been around since the age of dinosaurs, some of these ancient giant viruses are still around, too.

Giant viruses, as the name suggests, are much larger than other viral families: so much larger that, like bacteria, they can be seen under a regular microscope. Because of their size, they went undiscovered for years since scientists assumed they were bacteria. These viruses are much more cell-like, with thousands more genes than their tiny cousins, including those needed to make proteins and copy DNA. Giant viruses found in the ocean that infect plankton have been known to steal genes from their hosts, including genes necessary for metabolism.

These characteristics led some scientists to believe that giant viruses represented a fourth domain, or major group, of life. Evolutionary biology currently states that there are three major domains: Archaea, Bacteria, and Eukaryota. The first two are mostly single cell organisms while the third encompasses plants, fungi, and animals (including humans). This theory suggests that over time, cells shed genes and became parasitic, becoming gina viruses.

The fourth domain theory calls into question the very definition of a virus and, for that matter, of life. While this theory has been largely disproven, the existence of giant viruses adds weight to the idea that some viruses originated separately from cells. Although from what they derived exactly is difficult to say: ideas range from even larger, complex entities that shrank down over time, to microscopic gene thieves that grew larger to compensate for the extra ‘stuff’ they were carrying around. 

Giant viruses have typically been found in dark, cold places, like the permafrost or deep within ocean sediment. There, they can lay dormant for years under the right conditions. In 2013, a group of French scientists discovered giant virion particles in 30,000-year-old soil in the Siberian permafrost. When the “sleeping” virus was exposed to an amoeba in a lab, it ‘woke’ up and infected the cells. Viruses tend to degrade over time when exposed to light, heat, and biochemical degradation, but this virus remained intact despite its age, probably because it was frozen in permafrost. The French scientists named the virus they found the “Pithovirus.”

The discovery of the Pithovirus showed that giant viruses can have an incredible amount of diversity. But the diversity seen in viruses makes it hard to pin down their origins. In the years since giant viruses were first discovered, scientists have sequenced a variety of their genomes and found they contain material unique from not only cells, but even other viruses.

While it’s incredible that scientists were able to activate a 30,000-year-old virus, the experiment begs the question: Could these ancient viruses infect humans?

The answer is: well, maybe.

If the current COVID-19 pandemic has taught us anything, it’s that viruses can easily jump to a new host. But how they are discovered can vary. In the case of COVID-19, humans began to encroach on the habitats of bats, the original hosts of coronaviruses. For Pithovirus, on the other hand, climate change played a role: its discovery was made possible due to the melting of the permafrost.  Although, as far as we know, giant viruses only infect amoebas and bacteria, it’s possible that we could come across something that could infect humans. The chances of this happening only grows with continuous erosion and thawing caused by humans.

What’s more, the scientists who discovered Pithovirus found that it was similar enough to other pathogens and that it had the capability to infect animals and humans under the right circumstances. This is because giant viruses are still part of the group of viruses that infect our domain of life. However, the threat is very small.  The scientists concluded that rigorous testing and reviving giant viruses in a lab setting would provide us with valuable data and that helps us realistically assess whether these giants threaten our health.

While the coronavirus family has become synonymous with SARS-CoV-2, the particular strand that causes COVID-19 is actually part of a group of viruses that infect mammals, particularly bats, birds, and humans. Until very recently, scientists had estimated coronaviruses first appeared around 10,000 years ago. In evolutionary terms, this was quite late considering, their hosts have been evolving for millions of years.

But it turns out that the scientists who were investigating the age of these viruses, they didn’t take into account the unique ways that viruses mutate and redistribute their genes. When they updated their technique to account for the unique lineage of viruses, they found that the four major coronavirus groups originated much earlier than previously thought, by some tens of millions of years.

These findings also suggested that ancient coronaviruses may have infected the common ancestors of bats and birds before they split into separate species. Then, as the two families of animals diverged, the virus continued to adapt along with them. In fact, viruses may have even helped drive evolutionary change by altering their host’s DNA by either becoming a permanent feature or by forcing the host to develop defenses against the virus that lived within them. A large study of bat species in China found evidence of such complimentary evolution, noting that different sspecies of bats had developed different tactics of warding off various coronavirus mutations, to the point that the bats no longer get sick.

Viruses outnumber living things by the millions and have proven to be important in driving change among life on earth. They have altered the DNA of their hosts and have challenged humans to develop the best technology and medicine to subdue them. Viruses have been at the game for a long time, for millions of years. They are still developing new tricks like switching to new hosts or escaping from cells as a means to survive. By studying their origins, we can better understand their structures and their methods and maybe even figure out what they’ll do next.