A Planet of Viruses

by Carl Zimmer

  We have the jackalope to thank for this realization. The myth of the jackalope was one of the clues that led virologists to discover that some viruses cause cancer. In the 1960s, one of the most intensely studied cancer-causing viruses was avian leukosis virus. At the time, the virus was sweeping across chicken farms and threatening the entire poultry industry. Scientists found that avian leukosis virus belonged to a group of species known as retroviruses. Retroviruses insert their genetic material into their host cell’s DNA. When the host cell divides, it copies the virus’s DNA along with its own. Under the certain conditions, the cell is forced to produce new viruses—complete with genes and a protein shell—which can then escape to infect a new cell. Retroviruses sometimes trigger cells to turn cancerous if their genetic material is accidentally inserted in the wrong place in their host’s genome. Retroviruses have genetic “on switches” that prompt their host cell to make proteins out of nearby genes. Sometimes their switches turn on host genes that ought to be kept shut off, and cancer can result.

  Avian leukosis virus proved to be a very strange retrovirus. At the time, scientists tested for the presence of the virus by screening chicken blood for one of the virus’s proteins. Sometimes they would find the avian leukosis virus protein in the blood of chickens that were perfectly healthy and never developed cancer. Stranger still, healthy hens carrying the protein could produce chicks that were also healthy and also carried the protein.

  Robin Weiss, a virologist then working at the University of Washington, wondered if the virus had become a permanent, harmless part of the chicken DNA. He and his colleagues treated cells from healthy chickens with mutation-triggering chemicals and radiation to see if they could flush the virus out from its hiding place. Just as they had suspected, the mutant cells started to churn out the avian leukosis virus. In other words, these healthy chickens were not simply infected with avian leukosis virus in some of their cells; the genetic instructions for making the virus were implanted in all of their cells, and they passed those instructions down to their descendants.

  These hidden viruses were not limited to just one oddball breed of chickens. Weiss and other scientists found avian leukosis virus embedded in many breeds, raising the possibility that the virus was an ancient component of chicken DNA. To see just how long ago avian leukosis viruses infected the ancestors of today’s chickens, Weiss and his colleagues travelled to the jungles of Malaysia. There they trapped red jungle fowl, the closest wild relatives of chickens. The red jungle fowl carried the same avian leukosis virus, Weiss found. On later expeditions, he found that other species of jungle fowl lacked the virus.

  Out of the research on avian leukosis virus emerged a hypothesis for how it had merged with chickens. Thousands of years ago, the virus plagued the common ancestor of domesticated chickens and red jungle fowl. It invaded cells, made new copies of itself, and infected new birds, leaving tumors in its wake. But in at least one bird, something else happened. Instead of giving the bird cancer, the virus was kept in check by the bird’s immune system. As it spread harmlessly through the bird’s body, it infected the chicken’s sexual organs. When an infected bird mated, its fertilized egg also contained the virus’s DNA in its own genes.

  As the infected embryo grew and divided, all of its cells also inherited the virus DNA. When the chick emerged from its shell, it was part chicken and part virus. And with the avian leukosis virus now part of its genome, it passed down the virus’s DNA to its own offspring. The virus remained a silent passenger from generation to generation for thousands of years. But under certain conditions, the virus could reactivate, create tumors, and spread to other birds.

  Scientists recognized that this new virus was in a class of its own. They called it an endogenous retrovirus—endogenous meaning generated within. They soon found endogenous retroviruses in other animals. In fact, the viruses lurk in the genomes of just about every major group of vertebrates, from fish to reptiles to mammals. Some of the new endogenous retroviruses turned out to cause cancer like avian leukosis virus, but many did not. Some seemed to be effectively muzzled by their host. Certain endogenous retroviruses carried by mice cannot infect mice cells, for example, but they can readily spread among rat cells.

  Other endogenous retroviruses turned out to be crippled, carrying mutations that robbed them of the ability to make full-fledged viruses. They could still make new copies of their genes, however, which were then reinserted back into their host’s genome. And scientists also discovered some endogenous retroviruses that were so riddled with mutations that they could no longer do anything at all. They had become nothing more than baggage in their host’s genome.

  Endogenous retroviruses can linger in their hosts for millions of years. In 2009, Aris Katzourakis, an evolutionary biologist at the University of Oxford, discovered hundreds of copies of endogenous retroviruses in the genome of the three-toed sloth. Their genes closely matched those of foamy viruses, free-living pathogens that infect primates and other mammals. Katzourakis concluded that foamy viruses infected the common ancestor of three-toed sloths and primates, which lived a hundred million years ago. In primates, they’ve remained free-living. In the sloth lineage, however, they became trapped in their host’s DNA and have remained there ever since.

  As scientists discovered endogenous retroviruses in other species, they naturally wondered about our own DNA. After all, we suffer infections from many retroviruses. Virologists tried coaxing endogenous retroviruses out of human cells without any luck. But when they scanned the human genome, they found many segments of DNA that bore a striking resemblance to retroviruses. Many of those segments resembled retrovirus-like segments in apes and monkeys, suggesting that they had infected our ancestors thirty million years ago or more. But some of the retrovirus-like segments in the human genome had no counterparts in any other species. It was possible that the segments unique to humans started out as retroviruses that infected our ancestors a million years ago.

  To test this idea, Thierry Heidmann, a researcher at the Gustave Roussy Institute in Villejuif, France, tried to bring a human endogenous retrovirus back to life. Searching through the genomes of different people, he and his colleagues found slightly different versions of one retrovirus-like segment. These differences presumably arose after a retrovirus became trapped in the genomes of ancient humans. In their descendants, mutations struck different parts of the virus’s DNA.

  Heidmann and his colleagues compared the variants of the virus-like sequence. It was as if they found four copies of a play by Shakespeare, each transcribed by a slightly careless clerk. Each clerk might make his own set of mistakes. Each copy might have a different version of the same word—say, wheregore, sherefore, whorefore, wherefrom. By comparing all four versions, an historian could figure out that the original word was wherefore.

  Using this method, Heidmann and his fellow scientists were able to use the mutated versions in living humans to determine the original sequence of the DNA. They then synthesized a piece of DNA with a matching sequence and insert it into human cells they reared in a culture dish. Some of the cells produced new viruses that could infect other cells. In other words, the original sequence of the DNA had been a living, functioning virus. In 2006, Heidmann named the virus Phoenix, for the mythical bird that rose from its own ashes.

  Retroviruses are a major threat to human health when they’re free-living, but even after they become endogenous they remain dangerous. Mutations can give them back the ability to make full-blown viruses that can escape and cause new infections and even cause cancer. Endogenous retroviruses that can only insert new copies of their DNA into their host genome are dangerous as well, because they can cause genes that are shut down to switch on at the wrong times. The threat from endogenous retroviruses is so great, in fact, that our ancestors evolved weapons that exist only to keep these viruses from spreading.

  Paul Bieniasz, a virologist at Rockefeller University, discovered two of these weapons in 2007 by reviving an endogenous retrov
irus, as Hiedmann’s team had revived Phoenix the year before. Bieniasz dubbed his resurrected virus HERV-K[con]. When he infected human cells with it, he found that the cells could fight the virus using two proteins called APOBEC3. Bieniasz’s experiments suggest that APOBEC3 homes in on endogenous retroviruses as they are making new copies of themselves destined to be inserted back into the host’s genome. The protein upsets the gene-copying process so that the new copies of the viruses pick up extra mutations. The extra mutations act like a hail of bullets. Some of them don’t cause any harm, but if one of them hits a vital spot in the virus’s DNA, it can cripple the virus so that it can no longer reproduce.

  Proteins like APOBEC3 disable endogenous retroviruses, but they don’t eliminate them. Over millions of years, our genomes have picked up a vast amount of DNA from dead viruses. Each of us carries almost a hundred thousand fragments of endogenous retrovirus DNA in our genome, making up about 8 percent of our DNA. To put that figure in perspective, consider that the twenty thousand protein-coding genes in the human genome make up only 1.2 percent of our DNA. Scientists have also observed millions of smaller pieces of “jumping DNA” in the human genome. It’s possible that many of those pieces evolved from endogenous retrovirus, having been stripped down to the bare essentials required for copying DNA.

  Endogenous retroviruses may be dangerous parasites, but scientists have discovered a few that we have commandeered for our own benefit. When a fertilized egg develops into a fetus, for example, some of its cells develop into the placenta, an organ that draws in nutrients from the mother’s tissues. The cells in the outer layer of the placenta fuse together, sharing their DNA and other molecules. Heidmann and other researchers have found that a human endogenous retrovirus gene plays a crucial role in that fusion. The cells in the outer placenta use the gene to produce a protein on their surface, which latches them to neighboring cells. In our most intimate moment, as new human life emerges from old, viruses are essential to our survival. There is no us and them—just a gradually blending and shifting mix of DNA.

  THE VIRAL FUTURE

  The Young Scourge

  Human Immunodeficiency Virus

  Every week, the Centers for Disease Control and Prevention publish a thin newsletter called Morbidity and Mortality Weekly Report. The issue that appeared on July 4, 1981, was a typical assortment of the ordinary and the mysterious. Among the mysteries that week was a report from Los Angeles, where doctors had noticed an odd coincidence. Between October 1980 and May 1981, five men were admitted to hospitals around the city with the same rare disease, known as pneumocystis pneumonia.

  Pneumocystis pneumonia is caused by a common fungus called Pneumocystis jiroveci. The spores of P. jiroveci are so abundant that most people inhale it at some point during their childhood. Their immune system quickly kills off the fungus and produces antibodies that ward off any future infection. But in people with weak immune systems, P. jiroveci runs rampant. The lungs fill with fluid and become badly scarred. Its victims struggle to breathe enough oxygen to stay alive. The five Los Angeles patients did not fit the typical profile of a pneumocystis pneumonia victim. They were young men who had been in perfect health before they came down with pneumonia. Commenting on the report, the editors of Morbidity and Mortality Weekly Report speculated that the puzzling symptoms of the five men “suggest the possibility of a cellular-immune dysfunction.”

  Little did they know that they were publishing the first observations of what would become the greatest epidemic in modern history. The five Los Angeles men did indeed have a cellular-immune dysfunction, one that would turn out to be caused by a virus known today as human immunodeficiency virus (HIV). The virus, researchers would later discover, had been secretly infecting victims for fifty years. During the 1980s it finally exploded, and since then it has infected sixty million people. It has killed nearly half of them.

  HIV’s death toll is all the more terrifying because it’s actually not all that easy to catch. You can’t get HIV if an infected person sneezes near you or shakes your hand. HIV has to be spread through certain bodily fluids, such as blood and semen. Unprotected sex can transmit the virus. Contaminated blood supplies can infect people through transfusions. Infected mothers can pass HIV to their unborn children. Many people who take heroin and other drugs have acquired HIV if they’ve shared needles with infected users.

  Once HIV gets into a person’s body, it boldly attacks the immune system itself. It grabs onto certain kinds of immune cells known as CD4 T cells and fuses their membranes like a pair of colliding soap bubbles. Like other retroviruses, it inserts its genetic material into the cell’s own genome. Its genes and proteins manipulate then take over the cell, causing it to make new copies of HIV, which escape and can infect other cells.

  At first, the population of HIV in a person’s body explodes rapidly. Once the immune system recognizes infected cells it starts to kill them, driving the virus’s population down. To the infected person, the battle feels like a mild flu. The immune system manages to exterminate most of the HIV, but a small fraction of the viruses manages to survive by lying low. The CD4 T cells in which they hid continued grow and divide. From time to time, an infected CD4 T cell wakes up and fires a blast of viruses that infect new cells. The immune system attacks these new waves, but over time it becomes exhausted and collapses.

  It may take only a year for an immune system to fail, or more than twenty. But no matter how long it takes, the outcome is the same: people can no longer defend themselves against diseases that would never be able to harm a person with a healthy immune system. In the early 1980s, a wave of HIV-infected people began to come to hospitals with strange diseases like pneumocystis pneumonia.

  Doctors discovered the effects of HIV before they discovered the virus, dubbing it acquired immunodeficiency syndrome, or AIDS. In 1983, two years after the first AIDS patients came to light, French scientists isolated HIV from a patient with AIDS for the first time. More research firmly established HIV as the cause of AIDS. Meanwhile, doctors were discovering more cases of AIDS, both in the United States and abroad. Other great scourges, such as malaria and tuberculosis, are ancient enemies, which had been killing people for thousands of years. Yet HIV went from utter obscurity in 1980 to a global scourge in a matter of a few years. Here was an epidemiological mystery.

  To solve it, scientists began to sequence the genes of HIV they isolated from different patients. They examined HIV not just from the United States but from other countries around the world where it was beginning to spread as well. They drew evolutionary trees, with each strain of HIV a branch sprouting from a common ancestor. Researchers discovered that there was not one kind of HIV, but two. The vast majority of cases of HIV were caused by a strain that was dubbed HIV-1, and the rest were caused by a distinct form of the virus, called HIV-2. The two types of HIV could be distinguished in many ways, including the symptoms they caused: HIV-2 was much milder than HIV-1.

  HIV, scientists found, belongs to a large group of slow-growing retroviruses, known as lentiviruses. Lentiviruses infect many mammals, including cats, horses, cows, and monkeys. In 1991, Preston Marx of New York University and his colleagues discovered that HIV-2 was closely related to lentiviruses that infect an African species of monkey called sooty mangabeys. They concluded that HIV-2 descended from a mangabey lentivirus. In West Africa, where HIV-2 is most common, some people keep the monkeys as pets; others eat them. Infected mangabeys may have introduced their lentivirus into humans with a bite.

  It took scientists longer to pin down the origins of HIV-1, the strain that causes the vast majority of AIDS cases. That’s because the closest relatives of HIV-1 lived in primates that are much harder to study: chimpanzees. Relatively few chimpanzees live in captivity, and trying to get blood samples from chimpanzees in the wild can be a staggeringly hard job. They’re elusive, strong, and not fond of people with needles. Scientists had to develop new ways to test them for HIV, such as searching for the viruses in their feces. Slowly
, scientists amassed a collection of HIV-1–like lentiviruses from chimpanzees. Comparing the viruses to each other, they discovered that some strains of HIV-1 are more closely related to certain chimpanzee viruses that they are to other HIV-1 strains. The branchings of the viral tree suggest that HIV-1 actually evolved from chimpanzee viruses several times.

  But when did this transition happen? Some scientists tried to get an answer to that question by looking back at patients who had died mysteriously before the discovery of HIV. In 1988, for example, researchers discovered that a Norwegian sailor named Arvid Noe, who died in 1976, had HIV in his tissues. Reaching back further into HIV’s history was nearly impossible, because many of its earliest victims lived in poor countries and died without any careful medical tests that would identify unusual diseases like pneumocystis pneumonia.

  It turned out that the viruses replicating in living people offered some powerful clues to the origins of HIV. Through the 1990s, scientists at Los Alamos National Laboratory amassed a database of genetic sequences of HIV taken from thousands of patients. They could then use supercomputers to compare these viruses and figure out which mutations the viruses had acquired since they diverged from a common ancestor. By adding up these mutations, the researchers found that HIV gradually acquires mutations at a roughly regular rate. In other words, the mutations piled up like sand in an hourglass. By measuring how high the sand had piled up, they could estimate how much time had passed. They estimated that the common ancestor of HIV-1 existed in 1933.