A Planet of Viruses

by Carl Zimmer

  Shope’s experiment did more than show that the horns contained viruses. He also demonstrated that the viruses created the horns, crafting them out of infected cells. After this discovery, Shope passed on his rabbit tissue collection to Rous, who continued to work on it for decades. Rous injected virus-loaded liquid deep inside rabbits and found that it didn’t produce harmless horns. Instead, the rabbits developed aggressive cancers that killed them. For his research linking viruses and cancer, Rous won the Nobel Prize in Medicine in 1966.

  The discoveries of Shope and Rous led scientists to look at growths on other animals. Cows sometimes develop monstrous lumps of deformed skin as big as grapefruits. Warts grow on mammals, from dolphins to tigers to humans. And on rare occasions, warts can turn people into human jackalopes. In the 1980s, a teenage boy in Indonesia named Dede began to develop warts on his body, and soon they had completely overgrown his hands and feet. Eventually he could no longer work at a regular job and ended up as an exhibit in a freak show, earning the nickname “Tree Man.” Reports of Dede began to appear in the news, and in 2007 doctors removed thirteen pounds of warts from Dede’s body. They’ve had to continue to perform surgeries to remove new growths from his body since then. Dede’s growths, along with all the others on humans and mammals, turned out to be caused by a single virus—the same one that puts horns on rabbits. It’s known as the papillomavirus, named for the papilla (buds in Latin) that cells form when they become infected.

  In the 1970s, the German researcher Harald zur Hausen speculated that papillomaviruses might be a far bigger threat to human health than the occasional wart. He wondered whether they might also cause tumors in the cervixes of women. Previous studies on cases of cervical cancer revealed patterns that were similar to sexually transmitted diseases. Nuns, for example, get cervical cancer much less often than other women. Some scientists had speculated cervical cancer was caused by a virus spread during sex. Zur Hausen wondered if cancer-causing papillomaviruses were the culprit.

  Zur Hausen reasoned that if this were true, he ought to find virus DNA in cervical tumors. He gathered biopsies to study, and slowly sorted through their DNA for years. In 1983 he discovered genetic material from papillomaviruses in the samples. As he continued to study the biopsies, he found more strains of papillomaviruses. Since zur Hausen first published his discoveries, scientists have identified one hundred different strains of human papillomavirus (or HPV for short). For his efforts, zur Hausen shared the Nobel Prize for Physiology or Medicine in 2008.

  Zur Hausen’s research put human papillomaviruses in medicine’s spotlight, thanks to the huge toll that cervical cancer takes on the women of the world. The tumors caused by HPV grow so large that they sometimes rip the uterus or intestines apart. The bleeding can be fatal. Cervical cancer kills over 270,000 women every year, making it the third leading cause of death in women, surpassed only by breast cancer and lung cancer.

  All of those cases got their start when a woman acquired an infection of HPV. The infection begins when the virus injects its DNA into a host cell. HPV specializes in infecting epithelial cells, which make up much of the skin and the body’s mucous membranes. The virus’s genes ends up inside the nucleus of its host cell, the home of the cell’s own DNA. The cell then reads the HPV genes and makes the virus’s proteins. Those proteins begin to alter the cell.

  Many other viruses, such as rhinoviruses and influenza viruses, reproduce violently. They make new viruses as fast as possible, until the host cell brims with viral offspring. Ultimately, the cell rips open and dies. HPV uses a radically different strategy. Instead of killing its host cell, it causes the cell to make more copies of itself. The more host cells there are, the more viruses there are.

  Speeding up a cell’s division is no small feat, especially for a virus with just eight genes. The normal process of cell division is maddeningly complex. A cell “decides” to divide in response to signals both from the outside and the inside, mobilizing an army of molecules to reorganize its contents. Its internal skeleton of filaments reassembles itself, pulling apart the cell’s contents to two ends. At the same time, the cell makes a new copy of its DNA—3.5 billion “letters” all told, organized into 46 clumps called chromosomes. The cell must drag those chromosomes to either end of the cell and build a wall through its center. During this buzz of activity, supervising molecules monitor the progress. If they sense that the division is going awry—if the cell acquires a defect that might make it cancerous, for example—the monitor molecules trigger the cell to commit suicide. HPV can manipulate this complex dance by producing just a few proteins that intervene at crucial points in the cell cycle, accelerating it without killing the cell.

  Many types of cells grow quickly in childhood and then slow down or stop altogether. Epithelial cells, the cells that HPV infects, continue to grow through our whole life. They start out in a layer buried below the skin’s surface. As they divide, they produce a layer of new cells that pushes up on the cells above them. As the cells divide and rise, they become different than their progenitors. They begin to make more of a hard protein called keratin (the same stuff that makes up fingernails and horse hooves). Loaded with keratin, the top layer of skin can better withstand the damage from the sun, chemicals, and extreme temperatures. But eventually the top layer of epithelial cells dies off, and the next rising layers of epithelial cells take its place.

  This arrangement means that HPV has to try to live on a conveyor belt. As HPV-infected cells reproduce, they move upward, closer and closer to their death. The viruses sense when their host cells are getting close to the surface and shift their strategy. Instead of speeding up cell division, they issue commands to their host cell to make many new viruses. When the cell reaches the surface, it bursts open with a big supply of HPV that can seek out new hosts to infect.

  For most people infected with HPV, a peaceful balance emerges between virus and host. Fast-growing infected cells don’t cause people harm, because they get sloughed off. The virus, meanwhile, gets to use epithelial cells as factories for new viruses, which can then infect new hosts through skin-to-skin contact and sex. The immune system helps maintain the balance by clearing away some of the infected cells. (Dede’s tree-like growths were the result of a genetic defect that left his body unable to rein in the virus.)

  This balance between host and virus has existed for hundreds of millions of years. To reconstruct the history of papillomaviruses, scientists compare the genetic sequence of different strains and note which animals they infect. It turns out that papillomaviruses infect not just mammals, such as humans, rabbits, and cows, but other vertebrates as well, such as birds and reptiles. Each strain of virus typically only infects one or a few related species. Based on their relationships, Marc Gottschling of the University of Munich has argued that the first egg-laying land vertebrates— the ancestor of mammals, reptiles, and birds—was already a host to papillomaviruses three hundred million years ago.

  As the descendants of that ancient animal evolved into different lineages, their papillomaviruses evolved as well. Some research suggests that these viruses began to specialize on different kinds of lining in their hosts. The viruses that cause warts, for example, adapted to infect skin cells. Another lineage adapted to the mucosal linings of the mouth and other orifices. For the most part, these new papillomaviruses coexisted peacefully with their hosts. Two-thirds of healthy horses carry strains of papillomavirus called BPV1 and BPV2. Some strains evolved to be more prone to turn cancerous than others, but researchers can’t say why.

  For thousands of generations, papillomaviruses would specialize on certain hosts, but from time to time, they leap to new species. A number of human papillomaviruses are most closely related to papillomaviruses that infect distantly related animals, like horses, instead of our closest ape relatives. Nothing more than skin contact may have been enough to allow viruses to make the jump.

  When our own species first evolved in Africa about two hundred thousand years ago, our anc
estors probably carried several different strains of papillomaviruses. Representatives of those strains can be found all over the world. But as humans expanded across the planet—leaving Africa about fifty thousand years ago and reaching the New World by about fifteen thousand years ago—their papillomaviruses were continuing to evolve. We know this because the genealogy of some HPV strains reflect the genealogy of our species. The viruses that infect living Africans belong to the oldest lineages of HPV, for example, while Europeans, Asians, and Native Americans carry their own distinct strains.

  For about 199,950 of the past 200,000 years, our species had no idea that we were carrying HPV. That’s not because HPV was a rare virus—far from it: a 2008 study on 1,797 men and women found 60 percent of them had antibodies to HPV, indicating they had been infected with the virus at some point in their life. For the overwhelming majority of those people, the experience was harmless. Of the estimated 30 million American women who carry HPV, only 13,000 a year develop cervical cancer.

  In this cancer-stricken minority, the peaceful balance between host and virus is thrown off. Each time an infected cell divides, there’s a small chance it will mutate one of the genes that helps regulate the cell cycle. In an uninfected cell, the mutation would not do much harm. But a cell that’s already being pushed by HPV to grow faster is in a precarious state. What might otherwise be a harmless mutation transforms an infected cell into a precancerous one. The cell multiplies much faster than before. Its descendants grow so fast that the shedding of the top layer of epithelial cells is not enough to get rid of them. They form a tumor, which pushes out and down into the surrounding tissue.

  The best way to prevent most cancers is to reduce the odds that our cells will pick up dangerous mutations: quitting smoking, avoiding cancer-promoting chemicals, and eating well. But cervical cancer can be blocked another way: with a vaccine. In 2006, the first HPV vaccines were approved for use in the United States and Europe. They all contain proteins from the outer shell of HPV, which the immune system can learn to recognize. If people are later infected with HPV, their immune system can mount a rapid attack and wipe it out.

  The introduction of the vaccines has brought controversies of many flavors. The developers recommend the vaccines for girls in their early teens. Some parents have protested that such a policy promotes sex before marriage. In 2008, medical experts raised a different set of concerns in editorials in the New England Journal of Medicine. It takes many years for HPV to give rise to cancers, they pointed out, and so we don’t yet know how effective the vaccines will prove to be.

  Another potential problem is the fact that current HPV vaccines only target two strains of the virus. The choice makes a certain amount of sense for vaccine makers who have to balance costs and benefits, since those two strains cause about 70 percent of all cases of cervical cancer. But we humans are host to over a hundred different strains of HPV, which are constantly acquiring new mutations and swapping genes between one another. If vaccines decimate the two most successful strains, natural selection might well favor the evolution of other strains to take their place. Never underestimate the evolutionary creativity of a virus that can transform rabbits into jackalopes or men into trees.

  EVERYWHERE, IN ALL THINGS

  The Enemy of Our Enemy

  Bacteriophages

  People have known about viruses, or at least their effects, for as long as viruses have been making people sick. Scientists discovered viruses in the nineteenth century, and by the beginning of the twentieth, they had learned a few important things about them. They knew that viruses were infectious agents of unimaginably small size. They had begun to assign certain diseases, such as tobacco mosaic disease or rabies, to certain viruses. But the young science of virology was still parochial. It focused mainly on the viruses that worried people most: the ones that infect humans or the ones that infect the crops and livestock we raise for food. Virologists rarely looked beyond our little circle of experience.

  A clue to the true scope of viruses came in the middle of World War I. French soldiers were dying in droves, killed not just by Germans but also by bacteria. The microbes invaded their torn flesh, their food, and their drinking water. Their path was made easier by the worldwide flu epidemic in 1918. The flu weakened the defenses of its victims, allowing bacteria to infect their lungs. The soldiers spread the flu to civilians, and ultimately fifty million people died—many of them killed by bacteria.

  Today, doctors can treat all of these bacterial infections with antibiotics. But antibiotics would not be discovered until the 1930s. During World War I, doctors could only treat battlefield infections by cleaning wounds and, if that failed, amputating limbs. Their patients often died anyway.

  In 1917, in the midst of this carnage, the Canadian-born physician Felix d’Herelle discovered what seemed to him a medical miracle: a powerful substance that could wipe out bacteria. It was not an antibiotic. Instead, Herelle had discovered something that no one had ever imagined before: a virus that attacked not humans, or other animals, or even plants. He found a virus that made bacteria its host.

  Herelle made his discovery while investigating an outbreak of dysentery among French soldiers. As part of his analysis, he passed the stool of the soldiers through a filter. The filter’s pores were so small that not even the bacteria that caused the dysentery, known as Shigella, could slip through. Once Herelle had produced this clear, filtered fluid, he then mixed it with a fresh sample of Shigella bacteria and then spread the mixture of bacteria and clear fluid in petri dishes.

  The Shigella began to grow, but within a few hours Herelle noticed strange clear spots starting to form in their colonies. He drew samples from those spots and mixed them with Shigella again. More clear spots formed in the dishes. These spots, Herelle concluded, were bacteria battlegrounds in which viruses were killing Shigella and leaving behind their translucent corpses. Herelle believed his discovery was so radical that his viruses deserved a name of their own. He dubbed them bacteriophages, meaning “eaters of bacteria.” Today, they’re known as phages for short.

  The concept of bacteria-infecting viruses was so strange and so new that some scientists couldn’t believe it. Jules Bordet, a French immunologist who won the Nobel Prize in 1919, became Herelle’s most outspoken critic after he failed to find phages of his own. Instead of Shigella, Bordet used a harmless strain of Escherichia coli. He poured E. coli–laden liquid through fine filters, and then mixed the filtered liquid with a second batch of E. coli. The second batch died, just as they had in Herelle’s experiments. But then Bordet decided to see what would happen if he mixed the filtered liquid with the first batch of E. coli—that is, the one he had filtered in the first place. To his surprise, the first batch of E. coli was immune. Bordet believed that his failure to kill the bacteria meant that the filtered fluid did not contain phages. Instead, he thought, it contained a protein produced by the first E. coli. The protein was toxic to other bacteria, but not to the ones that made it.

  Herelle fought back, Bordet counterattacked, and the debate raged for years. It wasn’t until the 1940s that scientists finally found the visual proof that Herelle was right. By then, engineers had built electron microscopes powerful enough to let scientists see viruses. When they mixed bacteria-killing fluid with E. coli and put it under the microscopes, they saw that bacteria were attacked by phages. The phages had boxlike shells in which their genes were coiled, sitting atop a set of what looked like spider legs. The phages dropped onto the surface of E. coli like a lunar lander on the moon and then drilled into the microbe, squirting in their DNA.

  As scientists got to know phages better, it became clear that the debate between Herelle and Bordet was just a case of apples and oranges. Phages do not belong to a single species, and different phage species behave differently toward their hosts. Herelle had found a vicious form, called a lytic phage, which kills its host as it multiplies. Bordet had found a more benevolent kind of virus, which came to be known as a temperate phage. Temp
erate phages treat bacteria much like human papillomaviruses treat our skin cells. When a temperate phage infects its host microbe, its host does not burst open with new phages. Instead, the temperate phage’s genes are joined into the host’s own DNA, and the host continues to grow and divide. It is as if the virus and its host become one.

  Once in a while, however, the DNA of the temperate phage awakens. It commandeers the cell to make new phages, which burst out of the cell and invade new ones. And once a temperate phage is incorporated into a microbe, the host becomes immune from any further invasion. That’s why Bordet couldn’t kill his first batch of E. coli with the phage—it was already infected, and thus protected.

  Herelle did not wait for the debate over phages to end before he began to use them to cure his patients. During World War I, he observed that as soldiers recovered from dysentery and other diseases, the levels of phages in their stool climbed. Herelle concluded that the phages were actually killing the bacteria. Perhaps, if he gave his patients extra phages, he could eliminate diseases even faster.