I want to tell you a story about a virus. This one does not infect humans, but a humble alga that lives in the surface waters of the oceans, where it feasts on sunlight. This particular alga is called Emiliania huxleyi — Ehux to its friends — and it is a beautiful little being. Less than one hundredth of a millimetre in diameter, this lifeform fabricates dozens of tiny, ornate scales, which it uses as an outer covering, as an alternative to a shell. The scales are made of the mineral calcite, a form of limestone, and they are called coccoliths, from the Greek for “stone grains”. The group of lifeforms that it belongs to are known as coccolithophores — “bearers of coccoliths”.
When times are good, these algae can reach staggeringly large numbers. In the north Atlantic in 1998, an Ehux bloom extended over almost 1m square kilometres — that’s an area four times larger than the UK — and blooms covering thousands of square kilometres are common. When this happens, the seas turn milky, forming patches that are easily visible from space. Not bad when you consider that to see any single individual of this species, you would need a microscope.
Ehux has viruses, known as EhVs. As viruses go, these are huge — each one may have a diameter of around one ten-thousandth of a millimetre, which is tiny from a human perspective, but far more massive than most of their kind. Scanned with an electron microscope, they look like 20-sided dice.
When Ehux blooms, outbreaks of these viruses help to bring those blooms to an end. Infected algae split apart, their cells ruptured, their lives over. Their tiny stone scales drift down to the seafloor, where they accumulate. And accumulate.
The world’s largest accumulations of coccoliths are plain to see. The white cliffs of Dover, of the German island of Rügen, of the Normandy coast of France, of the Smoky Hill River of Kansas in the US — these are all built of chalk, and chalk is composed mostly of coccoliths that accumulated ages ago, in ancient seas, when what is now land was beneath the waves.
Perhaps few geological formations give such a dizzying sense of the vastness of time. The bulk of the planet’s chalk formations were deposited more than 65m years ago, during the late Cretaceous — creta is Latin for chalk — and took many million years to build up. Back then, Earth was a different world: dinosaurs were stomping about, flowering plants had only recently evolved into bloom, and the lofty peaks of the Himalayas had not yet been upheaved. And as I behold these cliffs, I find myself wondering whether viruses were the chief cause of death for the coccolithophores of the Cretaceous seas, as they are today — and whether viruses are, therefore, implicated in the making of the chalk.
Stalking viruses into deep time is tricky; their direct fossil record is scant and enigmatic. After all, you’re not hunting for T-Rex skeletons; you’re trying to find specks that are, at their most gigantic, around one thousandth of a millimetre in diameter. Experiments show that viruses can fossilise; in some circumstances, minerals precipitate directly on top of virus particles, thus generating ultra tiny stone structures. But detecting such things in old rocks takes a fancy microscope. And even if you find some, it’s hard to be certain what you’re looking at. Nanofossils are notoriously difficult to interpret, and at least to my untutored eye, images of putative fossil viruses from ancient rocks amount to a kind of inkblot test.
But while the fossil evidence is uncertain, genetic evidence supports the view that viruses are old. Indeed, viruses of some sort are thought to be ancient, to have evolved in tandem with, or soon after, the first lifeforms, sometime around 4bn years ago. EhVs themselves belong to a group that seems to have evolved on to the scene more than 1.5bn years ago — far earlier than coccolithophores, which only began to leave traces in rocks around 225m years ago. Besides, today, all lifeforms have viruses that infect them, and there is no reason to suppose that this has been different in the past.
Which would mean that it was not simply millions of years of coccolithophore blooms and milky seas, but also millions of years of viral infections bringing those blooms to a close. Perhaps it’s not the white cliffs of Dover so much as the white cliffs of Doom. Yet I find it wondrous to consider that, together, such small entities, the coccolithophores and their viral companions, could have altered the fabric of the planet, leaving behind a tangible legacy of such magnitude.
I want to tell you another story about a virus. This one infects tobacco plants, causing the leaves to become blotchy and deformed, and stunting the plants’ growth. Known as the tobacco mosaic virus, it is something of a celebrity: a decade ago, plant pathologists voted it the most important plant virus. Its popularity does not arise from the disease it causes, but from the central role it has played in the accumulation of knowledge over the past 120 years.
Looking back from today, there is no moment in the history of science when viruses were discovered. Instead, their existence and strange nature emerged slowly from the shadows in a process that took several decades. By the end of the 19th century, it was clear that the mosaic disease of tobacco was caused by an infectious entity so small that it passed through filters that strained out all known bacteria.
In 1898, a Dutch microbiologist, Martinus Beijerinck, suggested that this invisible entity was not a minute organism, but something else, something fundamentally different in character. At the time, his ideas did not take hold. But back then, the available technology severely restricted the means by which these entities could be probed.
By the end of the 1920s, the situation had begun to change. The new tools of molecular biology revealed tobacco mosaic virus to be a biological particle of some sort, although exactly what sort remained unclear. Then, for the first time, a team of German scientists rendered the invisible visible.
In 1939, they deployed the newly invented electron microscope, or “Übermikroskop”, to examine two plant viruses, one of which was tobacco mosaic. They discovered that it resembled a tiny stick, or as one researcher later described it, a “cigarette-shaped” rod. (The other, a virus that infects potatoes, looked like a small piece of string.) Subsequent workers would find viruses shaped like tiny moon landers, bottles, even lemons — not to mention the spiky spheres of coronaviruses or the 20-sided dice of the EhVs.
As time went on, it gradually became clear that viruses are a distinct class of biological entity. They lack the structures of living cells, and they have no metabolism. In other words, viruses neither eat nor excrete. They do not breathe. They do not grow. Instead, all virus particles consist of a small packet that contains genetic material. The packet is made of proteins (in some cases, it may then be enclosed in a fatty envelope). The genetic material is either DNA, or its sister molecule RNA, depending on the virus.
Out in the world on their own, virus particles are inert. They only become troublesome when they bump into a suitable lifeform, and the genetic material from the virus enters the host cell. What happens next depends on both the virus and the host; but at some point, the infected cell may begin to use the genetic material from the virus to make new virus particles, a process that is often lethal to the host.
In the early years, viruses were seen simply as bad news. And certainly, Covid-19 is just the latest addition to a long and gloomy list of human maladies caused by viruses. Smallpox, chickenpox, measles, mumps, rubella, polio, influenza, rabies, yellow fever, dengue, Ebola, Aids, West Nile fever, Zika fever, even most forms of cervical cancer — I could go on.
But as the ability to peer inside cells has grown, it has become clear that, as a group, viruses are far more than agents of sickness and death. They are also one of the most creative forces in the history of life. Part of this derives directly from the harm they cause: any lifeforms that can defend themselves against one virus or another will tend to leave more descendants than less fortunate beings.
Viruses have, therefore, led lifeforms to evolve an impressive array of antivirus defences. These run from the mundane to the exotic. Among the mundane: some bacteria have evolved mechanical protections that reduce the odds of getting infected in the first place — the microbial equivalent of mask-wearing. Some researchers have suggested a similar role for coccoliths, though the idea has not yet been confirmed.
More exotic defences include molecular scissors that chop up offending viral genes, as well as the complex immune systems of mammals and birds. (Molecular scissors, by the way, are now an essential tool in biomedical research, and their discovery has led to Nobel prizes.) Viruses may, in turn, evolve to evade these defences, generating an ongoing evolutionary dance — and, over time, molecular interactions of fantastic complexity.
But the deeper creativity of viruses comes from something altogether more strange. Viral genetic material can be incorporated into the genetic material of the host. Sometimes it stays there, and the viral genes become a permanent part of the host’s genetic endowment. By some estimates, as much as 8 per cent of the human genome has been accumulated this way (most of the incorporations took place deep in the evolutionary past).
Over time, most of these viral genes decay, becoming ghosts harmlessly haunting the genomes of their hosts. But from time to time, some of these once-viral-genes become repurposed, evolving new functions within the lifeform that they are now part of. Indeed, the development of the human placenta depends, in part, on a gene that was once part of a virus.
Viruses can also acquire genes from their hosts — as an infected cell begins to make new virus particles, some of its own genetic material may be added to that of the virus. If the virus goes on to infect another cell, these “extra” genes are transmitted too, potentially bestowing new genetic powers upon the recipient. It’s a kind of inheritance, but not the normal, parent-to-child sort.
And here’s the thing. The language of genes is universal: all lifeforms interpret genetic material in essentially the same way. A virus that can infect lifeforms that are only distantly related may sometimes, therefore, move genes across the tree of life. Such happenings accelerate evolution: lifeforms acquire new traits wholesale, rather than having to wait for them to come about. To give an example: some of the genes that allow organisms to convert the energy in sunlight into chemical energy appear to have moved around the tree of life in this way. But perhaps this is less surprising than it seems: because viruses are so numerous, and Earth history so long, events of this kind are bound to have happened from time to time.
Today, viruses are the planet’s most abundant biological entities. A droplet of seawater may contain more than 100m of them; a gram of soil, around 1bn. You can find viruses in sediments at the bottom of the ocean, in hot springs, and high in the air. Although only a few thousand have been formally described, there are thought to be millions of different kinds. Happily, the great bulk of these do not infect humans, but bacteria — which are themselves extremely numerous and diverse.
Ever since Beijerinck proposed that the mosaic disease of tobacco was caused by a new kind of entity, people have argued about whether viruses are alive. I have argued about it myself. I used to put them on the “life” side of the ledger. But now I would say it this way: viruses are of life, and they interact with life, but they are not alive. For one thing, all lifeforms can trace their origins back, across 4bn years, to a single common ancestor. Viruses cannot: they appear to have arisen several times independently. Coronaviruses and EhVs, for example, belong to groups that do not share an origin. When and how, and how often, new viral groups originate from scratch is, however, unknown.
In the midst of a global pandemic, such reflections are, perhaps, cold comfort. But I think it is fair to say that, had viruses never existed, we humans would not be here either. For better and for worse, they have helped to make our world.
Olivia Judson is the author of ‘Dr Tatiana’s Sex Advice to All Creation’ (Vintage). She is presently writing a history of life and Earth
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