A Planet of Viruses - Carl Zimmer (2011)

Introduction

“A Contagious Living Fluid”

Tobacco Mosaic Virus

Fifty miles southeast of the Mexican city of Chihuahua is a dry, bare mountain range called Sierra de Naica. In 2000, miners worked their way down through a network of caves below the mountains. When they got a thousand feet underground, they found themselves in a place that seemed to belong to another world. They were standing in a chamber measuring thirty feet wide and ninety feet long. The ceiling, walls, and floor were lined with smooth-faced, translucent crystals of gypsum. Many caves contain crystals, but not like the ones in Sierra de Naica. They measured up to thirty-six feet long apiece and weighed as much as fifty-five tons. These were not crystals to hang from a necklace. These were crystals to climb like hills.

Since its discovery, a few scientists have been granted permission to visit this extraordinary chamber, known now as the Cave of Crystals. Juan Manuel García-Ruiz, a geologist at the University of Granada, made the journey and figured out that the crystals formed when volcanoes began to form the mountains 26 million years ago. Subterranean chambers took shape and filled with hot mineral-laced water. The heat of the volcanic magma kept the water at around 136 degrees, the ideal temperature for the minerals to settle out of the water and form crystals. Somehow the water stayed at that perfect temperature for hundreds of thousands of years, allowing the crystals to grow to surreal sizes.

In 2009, another scientist, Curtis Suttle, paid a visit to the Cave of Crystals. Suttle and his colleagues scooped up water from the chamber’s pools and brought it back to their laboratory at the University of British Columbia to analyze. When you consider Suttle’s line of work, his journey might seem like a fool’s errand. Suttle has no professional interest in crystals, or minerals, or any rocks at all for that matter. He studies viruses.

There are no people in the Cave of Crystals for the viruses to infect. There are not even any fish. The cave has been effectively cut off from the biology of the outside world for millions of years. Yet Suttle’s trip was well worth the effort. After he prepared his samples of crystal water, he put them under a microscope and saw protein shells loaded with genes. Each drop of cave water may hold two hundred million viruses.

Just about wherever scientists look—deep within the earth, on grains of sand blown off of the Sahara Desert, under mile-thick layers of Antarctic ice—they find viruses. And when they look in familiar places, they find new ones. In 2009, Dana Willner, a biologist at San Diego State University, led a virus-hunting expedition into the human body. The scientists had ten people cough up sputum and spit it into a cup. Five of the people were sick with cystic fibrosis, and five were healthy. Out of that fluid, Willner and her team fished out fragments of DNA, which they compared to databases of the tens of millions of genes already known to science. Before Willner’s study, the lungs of healthy people were believed to be sterile. But Willner and her colleagues discovered that all their subjects, sick and healthy alike, carried viral menageries in their chests. On average, each person had 174 species of viruses in the lungs. But only 10 percent of those species bore any close kinship to any virus ever found before. The other 90 percent were as strange as anything lurking in the Cave of Crystals.

The science of virology is still in its early, wild days. Scientists are discovering viruses faster than they can make sense of them. And yet this is a late-blooming youth, for we have known about viruses for thousands of years. We have known them from their effects, in our sicknesses and our deaths. But for centuries we did not know how to join those effects to their cause. The very word virus began as a contradiction. We inherited the word from the Roman Empire, where it meant, at once, the venom of a snake or the semen of a man. Creation and destruction in one word.

Over the centuries, virus took on another meaning: it signified any contagious substance that could spread disease. It might be a fluid, like the discharge from a sore. It might be a substance that traveled mysteriously through the air. It might even impregnate a piece of paper, spreading disease with the touch of a finger. Virus only began to take on its modern meaning as the nineteenth century came to a close, thanks to an agricultural catastrophe. In the Netherlands, tobacco farms were swept by a disease that left plants stunted, their leaves a mosaic of dead and live patches of tissue. Entire farms had to be abandoned.

In 1879, Dutch farmers came to Adolph Mayer, a young agricultural chemist, to beg for help. Mayer carefully studied the scourge, which he dubbed tobacco mosaic disease. He investigated the environment in which the plants grew—the soil, the temperature, the sunlight. He could find nothing to distinguish the healthy plants from the sick ones. Perhaps, he thought, the plants were suffering from an invisible infection. Plant scientists had already demonstrated that fungi could infect potatoes and other plants, so Mayer looked for fungus on the tobacco plants. He found none. He looked for parasitic worms that might be infesting the leaves. Nothing.

Finally Mayer extracted the sap from sick plants and injected drops into healthy tobacco. The healthy plants, Mayer discovered, turned sick as well. Some microscopic pathogen must be multiplying inside the plants. Mayer took sap from sick plants and incubated it in his laboratory. Colonies of bacteria began to grow and became large enough that Mayer could see them with his naked eye. Mayer applied the bacteria to healthy plants to see if it would trigger tobacco mosaic disease. It failed. And with that failure, Mayer’s research ground to a halt.

A few years later, another Dutch scientist named Martinus Beijerinck picked up where Mayer left off. He wondered if something other than bacteria was responsible for tobacco mosaic disease, something far smaller. He ground up diseased plants and passed the fluid through a fine filter that blocked both plant cells and bacteria. When he injected the clear fluid into healthy plants, they became sick.

Beijerinck filtered the juice from the newly infected plants and found that he could infect still more tobacco. Something in the sap of the infected plants—something smaller than bacteria— could replicate itself and could spread disease. Beijerinck called it a “contagious living fluid.”

Whatever that contagious living fluid carried was different from any other kind of life biologists knew about. It was not only inconceivably small but also remarkably tough. Beijerinck could add alcohol to the filtered fluid, and it would remain infective. Heating the fluid to near boiling did it no harm. Beijerinck soaked filter paper in the infectious sap and let it dry. Three months later, he could dip the paper in water and use the solution to sicken new plants.

Beijerinck used the word virus to describe the mysterious agent in his contagious living fluid. It was the first time anyone used the word the way we do today. But in a sense, Beijerinck simply used it to define viruses by what they were not. They were not animals, plants, fungi, or bacteria. What exactly they were, Beijerinck could not say. He had reached the limits of what nineteenth-century science could reveal.

A deeper understanding of viruses would have to wait for better tools and better ideas. Electron microscopes allowed scientists to see viruses for what they are: particles of a nearly inconceivably small size. For comparison, tap out a single grain of salt from a shaker. You could line up about ten skin cells along one side of it. You could line up about a hundred bacteria. Compared to viruses, however, bacteria are giants. You could line up a thousand viruses alongside that same grain of salt.

Despite the small size of viruses, scientists discovered ways to dissect them and peer inside. A human cell is stuffed with millions of different molecules that it uses to sense its surroundings, crawl hither and yon, take in food, grow, and decide whether to divide in two or kill itself for the good of its fellow cells. Virologists found that many of the viruses they studied were just protein shells holding a few genes. They discovered that viruses can replicate themselves, despite their paltry genetic instructions, by hijacking other forms of life. They could see viruses inject their genes and proteins into a host cell, which they manipulated into producing new copies of the virus. One virus might go into a cell, and within a day a thousand viruses came out.

Virologists had grasped these fundamental facts by the 1950s. But virology did not come to a halt. For one thing, virologists knew little about the many different ways in which viruses make us sick. They didn’t know why papillomaviruses can cause horns to grow on rabbits and cause hundreds of thousands of cases of cervical cancer each year. They didn’t know what made some viruses deadly and others relatively harmless. They had yet to learn how viruses evade the defenses of their hosts and how they evolve faster than anything else on the planet. In the 1950s they did not know that a virus that would later be named HIV had already spread from chimpanzees into our own species, or that thirty years later it would become one of the greatest killers in history. They could not have dreamed of the vast numbers of viruses that exist on Earth; they could not have guessed that most of the genetic diversity of life can be found in virus genes. They did not know that viruses help produce much of the oxygen we breathe and help control the planet’s thermostat. And they certainly would not have guessed that the human genome is partly composed from thousands of viruses that infected our distant ancestors, or that life as we know it may have gotten its start four billion years ago from viruses.

Now scientists know these things—or, to be more precise, they know of these things. They now recognize that from the Cave of Crystals to the inner world of the human body, this is a planet of viruses. Their understanding is still rough, but it is a start. So let us start as well.