by Carl Zimmer
That estimate has been confirmed by the remarkable discovery of HIV preserved in tissues stored away in hospitals in Kinshasa, the capital of the Democratic Republic of the Congo in central Africa. In 1998, David Ho and his colleagues at Rockefeller University reported that they had isolated HIV from a blood sample taken from a patient in Kinshasa in 1959. In 2008, Michael Worobey and his colleagues at the University of Arizona discovered HIV in a second tissue sample from another pathology collection in Kinshasa, dating back to 1960. These two samples allowed researchers to confirm that HIV emerged in the early 1900s.
The molecular clock created by the Los Alamos researchers was accurate enough to predict the age of the Kinshasa viruses based on their genetic sequence alone. But the two viruses also provide a surprising glimpse at the diversity of HIV in Kinshasa around 1960. Worobey and his colleagues found that the old viruses were not closely related to each other. Instead, they were each closely related to a different branch of HIV-1 found in patients today. Studying the distant kinship of these two viruses, Worobey and his colleagues concluded that all of the major branches of HIV-1 found in the world today already existed in 1960. What’s more, they were all probably circulating around Kinshasa.
All this evidence is now pointing to how HIV-1 got its start. HIV-1-like viruses had been circulating among populations of chimpanzees throughout Africa. Hunters sometimes killed chimpanzees for meat, and from time to time they became infected by the viruses. But these hunters, living in relative isolation, were a dead end for the viruses. In the early 1900s the opportunities for these viruses changed as colonial settlements in central Africa began to expand to cities of ten thousand people or more. Commerce along the rivers allowed pathogens to reach the cities from remote forests. The chimpanzees carrying viruses most closely related to HIV-1 live today in the jungles of southeast Cameroon. It may be no coincidence that the rivers of that region flow south and eventually reach Kinshasa.
In the growing city of Kinshasa (then known as Leopoldville), HIV-1 could multiply. Instead of a few dead ends, it found a population that could sustain it and inside of which it could evolve into new forms better adapted to humans. By 1960, HIV-1 had bloomed into a wide genetic diversity, although it probably only infected a few thousand people.
Worobey and his colleagues have started to map the subsequent spread of HIV-1 out from Kinshasa to the rest of the world. The most common strain of HIV in the United States, for example, is known as HIV-1 subtype B. The oldest lineages of HIV-1 subtype B are found in Haiti, and Worobey estimates they branched off from African strains in the 1960s. That happens to be a time when many Haitians who had been working in the Congo returned to their homeland after the country became independent from Belgium. They may have unwittingly brought HIV back to the New World with them. Haitian immigrants or American tourists may have then brought HIV to the United States. The oldest lineages of HIV-1 subtype B in the United States, Worobey and his colleagues found, date back to about 1970. That’s about four decades since the virus became established in humans, and about one decade before five men in Los Angeles became sick with a strange form of pneumonia.
By the time scientists recognized HIV in 1983, in other words, the virus had already begun to turn into a global catastrophe. As a result, HIV has had a huge head start on scientists who hope to halt its spread. It would not be until the early 1990s that some strategies began to show real promise for slowing the epidemic. Changing people’s behaviors has proven effective. Uganda launched a major campaign against HIV that featured condom use and other public health measures. As a result, the country reduced its HIV rate from about 15 percent in the early 1990s to about 5 percent in 2001. Unfortunately funding for these programs began to ebb after a few years, and the infection rate in Uganda has begun to rise again.
Other researchers have investigated medications that can slow the rise of HIV in infected people, so that their immune systems can remain strong enough to block the onset of AIDS. Millions of people now take a cocktail of drugs that interfere with the ability of HIV to infect immune cells and use them to replicate. In affluent countries like the United States, these drug therapies have allowed some people to enjoy a relatively healthy life. But the cost of these drugs has meant that most people with HIV—living in the poorest countries—cannot afford a treatment that might give them extra years or even decades of life. That’s beginning to change rapidly, as the United States and nongovernmental organizations are now starting to provide these drugs to the most afflicted countries and as treatment programs are starting to be scaled up dramatically.
Yet these drugs, even if they can prolong lives, are not the perfect cure. They have side effects that can become harmful after years of therapy, and they foster the evolution of resistant viruses, which then requires shifting patients to new drugs. In theory, the best solution to HIV would be a vaccine—either one that could prevent people from becoming infected with the virus or one that could stimulate the immune system of infected people to attack it effectively. Vaccines would be far less expensive than treating HIV infection with drug cocktails and could help slow down the transmission cycle. But the quest for an HIV vaccine has been a disappointing struggle so far. In 2008, for example, a highly anticipated trial of a vaccine developed by Merck had to be abandoned because the vaccine appeared to be making people more likely to acquire HIV, not less.
There’s good reason to worry about any HIV vaccine, even one that shows promise in small trials. That’s because HIV is evolving in overdrive. HIV belongs to a group of viruses—including influenza—that are very sloppy in their replication. They create many mutants in very little time. These mutants provide the raw material for natural selection to act on, producing viruses that are better and better adapted. Within a single host, natural selection can improve the ability of viruses to escape detection of the immune system.
In 2008, Philip Goulder, a medical researcher at Oxford, led an international team of scientists who found evidence for the ongoing evolution of HIV. They studied the immune systems of 2,800 people from all over the world, examining proteins known as human leukocyte antigens, which infected cells use to transport fragments of viruses to their surface. The fragments can then be recognized by immune cells, which destroys the infected cell. Different people carry different variations in the genes for human leukocyte antigens. Goulder and his colleagues found that most of the HIV in each country carried mutations to the most effective human leukocyte antigens in that country’s population. Their findings tell us that HIV is rapidly adapting to the variations in human immune systems around the world. That is sobering news to those who are trying to build HIV vaccines. If a vaccine ever succeeds in boosting an effective immune response in people, HIV might well evolve a way to escape.
It’s possible that vaccine developers could keep HIV from escaping by continually rolling out new vaccines that would stay one step ahead of the virus. Another intriguing possibility is to look back over its history. A team of American scientists compared a wide range of HIV-1 subtype B strains and reconstructed one of the proteins made by their common ancestor. They then used that ancestral protein to make a vaccine. The researchers found that monkeys injected with the vaccine were able to produce an immune response to a much wider range of HIV strains than more conventional vaccines. The future of fighting HIV, perhaps, may lie in its past.
Becoming an American
West Nile Virus
In the summer of 1999, Tracey McNamara got worried. McNamara was the chief pathologist at the Bronx Zoo. When an animal at the zoo died, it was her job to figure out what killed it. She began to see dead crows on the ground near the zoo, and she wondered if they were being killed by some new virus spreading through the city. If the crows were dying, the zoo’s animals might start to die too.
Over Labor Day weekend, her worst fears were realized: three flamingoes died suddenly. So did a pheasant, a bald eagle, and a cormorant. McNamara examined the dead birds and found they had all suffered blee
ding in their brains. Their symptoms suggested that they had been killed by the same pathogen. But McNamara could not figure out what pathogen was responsible, so she sent tissue samples to government laboratories. The government scientists ran test after test for the various pathogens that might be responsible. For weeks, the tests kept coming up negative.
Meanwhile, doctors in Queens were seeing a worrying number of cases of encephalitis—an inflammation of the brain. The entire city of New York normally only sees nine cases a year, but in August 1999, doctors in Queens found eight cases in one weekend. As the summer waned, more cases came to light. Some patients suffered fevers so dire that they became paralyzed, and by September nine had died. Initial tests pointed to a viral disease called Saint Louis encephalitis, but later tests failed to match the results.
As doctors struggled to make sense of the human outbreak, McNamara was finally getting the answer to her own mystery. The National Veterinary Services Laboratory in Iowa managed to grow viruses from the bird tissue samples she had sent them from the zoo. They bore a resemblance to the Saint Louis encephalitis virus. McNamara wondered now if both humans and birds were succumbing to the same pathogen. She convinced the Centers for Disease Control and Prevention to analyze the genetic material in the viruses. On September 22, the CDC researchers were stunned to find that the birds were not killed by Saint Louis encephalitics. Instead, the culprit was a pathogen called West Nile virus, which infects birds as well as people in parts of Asia, Europe, and Africa. No one had imagined that the Bronx Zoo birds were dying of West Nile virus, because it had never been seen in a bird in the Western Hemisphere before.
Public health workers puzzling over the human cases of encephalitics decided it was time to broaden their search as well. Two teams—one at the CDC and another led by Ian Lipkin, who was then at the University of California, Irvine—isolated the genetic material from the human viruses. It was the same virus that was killing birds: West Nile. And once again, it took researchers by surprise. No human in North or South America had ever suffered from it before.
The United States is home to many viruses that make people sick. Some are old and some are new. When the first humans made their way into the Western Hemisphere some fifteen thousand years ago, they brought a number of viruses with them. Human papillomavirus, for example, retains traces of its ancient emigration. The strains of the virus found in Native Americans are more closely related to each other than they are to HPV strains in other parts of the world. Their closest relative outside of the New World are strains of HPV found in Asia, just as Native Americans are most closely related to Asians.
Columbus’s discovery of the New World triggered a second wave of new viruses. Europeans brought viruses causing diseases such as influenza and smallpox that wiped out most Native Americans. In later centuries, still more viruses arrived. HIV came to the United States in the 1970s, and at the end of the twentieth century, West Nile virus became one of America’s newest immigrants.
It had only been six decades since West Nile virus was discovered anywhere on the planet. In 1937, a woman in the West Nile district of Uganda came to a hospital with a mysterious fever, and her doctors isolated a new virus from her blood. Over the next few decades, scientists found the same virus in many patients in the Near East, Asia, and Australia. But they also discovered that West Nile virus did not depend on humans for its survival. Researchers detected the virus in many species in birds, where it could multiply to far higher numbers.
At first it was not clear how the virus could move from human to human, from bird to bird, or from bird to human. That mystery was solved when scientists found the virus in a very different kind of animal: mosquitoes. When a virus-bearing mosquito bites a bird, it sticks its syringe-like mouth into the animal’s skin. As the mosquito drinks, it squirts saliva into the wound. Along with the saliva comes the West Nile virus.
The virus first invades cells in the bird’s skin, including immune system cells that are supposed to defend animals from diseases. Virus-laden immune cells crawl into the lymph nodes, where they release their passengers, leading to the infection of more immune cells. From the lymph nodes, infected immune cells spread into the bloodstream and organs such as the spleen and kidneys. It takes just a few days for the viruses in a mosquito bite to multiply into billions inside a bird. Despite their huge numbers, West Nile viruses cannot escape a bird on their own. They need a vector. An mosquito must bite the infected bird, drawing up some of its virus-laden blood. Once in the mosquito, the viruses invade the cells of its midgut. From there they can be carried to the insect’s salivary glands, where the viruses are ready to be injected into a new bird.
Vector-borne viruses like West Nile virus require a special versatility to complete their life cycle. Mosquitoes and birds are profoundly different kinds of hosts, with different body temperatures, different immune systems, and different anatomies. West Nile virus has to be able to thrive in both environments to complete its life cycle. Vector-borne viruses also pose special challenges to doctors and public health workers who want to stop their spread. They don’t require people to be in close contact to spread from host to host. Mosquitoes, in effect, give the viruses wings.
Studies on the genes of West Nile virus suggest that it first evolved in Africa. As birds migrated from Africa to other continents in the Old World, they spread the virus to new bird species. Along the way, West Nile virus infected humans. In Eastern Europe, epidemics broke out, producing some cases of encephalitis. In a 1996 epidemic in Romania, ninety thousand people came down with West Nile, leading to seventeen deaths. These new epidemics, first in Europe and later in the West, may have been the result of the virus infecting people who populations had not experienced it before. In Africa, by contrast, people may be immunized against West Nile virus after being infected while they’re young.
It is striking that the New World has been spared West Nile virus for so long. The flow of people across the Atlantic and Pacific was not enough to carry the virus to the Americas. Scientists cannot say exactly how West Nile virus finally landed in New York in 1999, but they have a few clues. The New World strain of West Nile virus is most closely related to viruses that caused an outbreak in birds in Israel in 1998. It’s possible that pet smugglers brought infected birds from the Near East to New York.
On its own, a single infected bird could not have triggered a nationwide epidemic. The viruses needed a new vector to spread. It just so happens that West Nile viruses can survive inside 62 species of mosquitoes that live in the United States. The birds of America turned out to be good hosts as well. All told, 150 American bird species have been found to carry West Nile virus. A few species, such as robins, blue jays, and house finches, turned out to be particularly good incubators.
Moving from bird to mosquito to bird, West Nile virus spread across the entire United States in just 4 years. And along the way, people became ill with West Nile virus as well. About 85 percent of infections in the United States cause no symptoms. The other 15 percent of infected people develop fevers, rashes, and headaches, and 38 percent of them have to go to a hospital, where they stay for about 5 days on average. About 1 in 150 infected people end up developing encephalitis. Between 1999 and 2008, U.S. doctors recorded 28,961 cases of West Nile virus. Of those victims, 1,131 died.
Once West Nile virus arrived in the United States, it settled into a regular cycle, a cycle set by the natural history of birds and mosquitoes. In the spring, robins and other birds produce new generations of chicks that are helpless targets for virus-carrying mosquitoes. By the summer, many birds are positively brimming with West Nile virus, raising the fraction of mosquitoes that carry it. It’s at that time of year that most human cases of West Nile virus emerge. When the temperature falls, mosquitoes die, and the viruses can no longer spread. It’s not clear how the virus survives North American winters. It’s possible that they survive in low levels among mosquitoes in the south, where the winters aren’t so harsh. It’s also possible that mosq
uitoes infect own their eggs with West Nile virus. When infected eggs hatch the next spring, the new generation is ready to start infecting birds all over again.
West Nile virus has fit so successfully into the ecology of the United States that it’s probably going to be impossible to eradicate. Unfortunately, doctors have no vaccine to prevent West Nile virus and no drugs to treat an infection. If you get sick, you can only hope that you are among the majority who suffer a fever and then recover. And in the future, West Nile virus may become even more entrenched in its new home. Jonathan Soverow of Beth Israel Deaconess Medical Center and his colleagues examined sixteen thousand cases of West Nile virus that occurred between 2001 and 2005, noting the weather at the time of each outbreak. They found that epidemics tended to occur when there was heavy rainfall, high humidity, and warm temperatures. Warm, rainy, muggy weather makes mosquitoes reproduce faster and makes their breeding season longer. It also speeds up the growth of the viruses inside the mosquitoes.