By spring of this year, Jeffery Taubenberger expects to have in hand the entire genetic sequence of the influenza virus responsible for 1918’s devastating global epidemic. Taubenberger, a molecular pathologist at the Armed Forces Institute of Pathology in Rockville, Maryland, is using the 1918 flu genome information to answer lingering mysteries about the flu virus, such as where it originated, why it was so virulent, and why it struck with such ferocity among presumably healthy young adults. Already, he and other researchers have come up with some intriguing clues:

The Origin

The influenza A virus, the particular type of influenza that causes illness in humans, occurs naturally and without symptoms or disease in waterfowl like duck and geese. Taubenberger’s analysis of the 1918 strain showed that the hemagglutinin protein, one of two receptor proteins on the surface of the virus capsule which helps it gain entry into host cells, was similar to the proteins of bird flu strains, but yet was not identical. That led Taubenberger to suspect that the pandemic virus had either jumped right from birds in 1918 (as happened in the 1957 and 1968 influenza pandemics) and then rapidly mutated, or originally came from a wild bird but spent quite a bit of time in an intermediate host susceptible to flu infection — a domestic chicken, say, or a pig — before making the move to people. Taubenberger eventually ruled out the idea of an intermediate host. He and his colleagues searched for a natural host for the 1918 strain by examining hundreds of ducks and water birds dating from around 1918 that had been preserved in ethanol and stored at the Smithsonian Institution. “We found a number of birds that were positive in our molecular analysis for influenza, but the genes looked basically identical to those isolated from modern birds,” Taubenberger says, and none looked like the killer 1918 virus, which makes a rapidly changing bird flu virus an unlikely source of the pandemic bug. “Our current theory is that the 1918 virus derived from an animal source of influenza that has not yet been identified. It could certainly be a bird, but it is not your typical bird flu host, like ducks, geese, and shore birds. It’s still a mystery.”

The Spread

This illustration shows the influenza virus penetrating the wall of a human cell.

The 1918 virus’s virulence — its exceptional ability to infect and swiftly spread through the population — also remains something of a puzzle. Taubenberger and his colleagues have found that one particular virus protein, called NS1, seemed to increase the virulence of the bug by temporarily dampening the host’s immune system, so the virus can get into cells, replicate, and spread through the body. In early February, British researchers reported uncovering another potential cause for the virus’s deadly efficiency. Using Taubenberger’s gene sequence, the team recreated the hemagglutinin protein and analyzed its structure. They found that the protein had been slightly altered compared to similar bird flu strains, a modification that allowed it to bind particularly well to human cells.

The Deadly Toll

Unfortunately, the sequences of the 1918 flu genes offer no explanation for why the most deaths in the pandemic were among young adults, 18-35 years old — a population that traditionally has the lowest influenza death rate. Taubenberger suspects that the virus’s lethality had less to do with its genetic sequence than with an unusual immune response to it in its victims. The idea is that prior exposure to a different strain of virus — an earlier case of the flu — caused their body to react improperly to the 1918 bug, perhaps allowing it to replicate and infect cells and tissues even faster than it normally would have. “It made them particularly susceptible to die,” he says.

“In a way, such an immune response makes a 1918-type pandemic less likely to reappear. If it is not just a feature of the virus, but the virus plus some set of really odd conditions that had to be lined up before this happened, the chances of all those dominoes being lined up in the right order again seems unlikely. But that’s not very satisfying. Obviously, you want a firm answer.”

Other researchers also suspect a unique link between flu and the human immune system, but one that affects the virus, not its human host. Last spring, molecular evolutionist Robin Bush of the University of California at Irvine, biological modeler Neil Ferguson of Imperial College London, and their colleagues published a mathematical model that explains how new strains of influenza appear. Compared with other organisms, the influenza A virus has an odd evolutionary pattern; it mutates rapidly to form new strains, but then nearly all the variants quickly die out, producing a stick-straight evolutionary tree rather than a typical branching bush. Only one strain is dominant at a time, all over the world; other strains can’t get a foothold. The dominant strain can change in a heartbeat, though, which is why vaccine developers have to be diligent about the viral targets of the shots. Bush and her colleagues found that the unique pattern could only be explained if the human immune system plays a key role. “The only thing that produced this pattern in our model was to have a generalized host immune response that did not let you get any kind of flu for a couple of weeks after you had it,” she says. New strains that arise during the outbreak therefore have no one to infect, and die out. Although immunologists have no clear evidence that the immunity exists — or any idea of how it works — the theory has fabulous potential; exploiting that response could someday lead to new types of super-vaccines that, for example, would ramp up the immune system to maintain that short-term protection over the long haul to completely stave off the flu.

These photos show the flu vaccine under development, and the usual method of vaccination.

Such vaccines, if even possible, are at least decades in the future, and that doesn’t help flu specialists now faced with the looming threat of another pandemic like 1918’s. “Nobody can say with certainty that there will be another pandemic, but if you go back several hundred years in history it looks like, on average, a pandemic emerges every 30 years,” Taubenberger says. The last pandemic was in 1968 — 36 years ago. “We can’t fully predict the future, but I think it is quite likely that a pandemic will occur again just because they have occurred in the past. What also makes it more likely is that we have more intense agricultural practices, these megafarms where you have many thousands of animals in close proximity, which makes it easier for the virus to get into animals and spread” — both within species and to other susceptible species, like humans.

Nor does the promise of a super-vaccine help researchers deal with the next flu season. During this past flu season, the influenza vaccine didn’t quite hit the mark; the flu that raged through the winter was a new, or “drifted,” strain not targeted by the vaccine. According to a preliminary study by the Centers for Disease Control of vaccinated healthcare workers in Colorado, the vaccine was not effective or had very low effectiveness against “influenza-like illness” in a group of healthcare workers in Colorado. “The problem was one of mechanics,” says Robin Bush. “There is a huge time lag between when the strain selection is made in February and upcoming flu season. It takes from then until the fall to develop the virus, grow it in culture, get FDA approval, etc. And during that lag time, our summer, it is flu season in the southern hemisphere and the strain can change.”

“The surveillance network that exists, founded by the World Health Organization, is really excellent at looking at influenza in humans and identifying strains that are mutants from the dominant one and might emerge in the next year or two as the one they want to base a vaccine on,” Taubenberger says. “The decisions are difficult but nine out of ten times they get it right. More surveillance, more data, would be good, but there also should be increased surveillance at the animal-human interface, of people who interact with animals at live food markets in Southeast Asia, or farmers who are involved with animals that can be host to the flu. We need to see how often these people are exposed to influenza virus, what the rate of infection is, etc, because it looks like these pandemic viruses form when influenza viruses move from animals into humans. It’s an economic issue too, and there are limited resources, but I think that influenza really needs to be thought of as a major public health problem, and it normally is not. People use the term ‘flu’ rather lightly and equate it with a cold, although just a normal flu makes you really ill.”

Molecular pathologist has spent much of the past eight years immersed in the genetic analysis of the virus responsible for the 1918 influenza pandemic. Before he began his landmark investigation to decipher the virus’s mysteries, including where it originally came from and why it was so deadly, Taubenberger knew remarkably little about the virus and the outbreak. “The only thing I remembered was a brief passage from my medical school training that it was the worst pandemic in history and that at least 20 million people had died, but beyond that I had really sketchy details in my mind,” he recalls. “It is curious that the pandemic doesn’t seem to be part of the cultural memory, at least in the United States, although it was a huge event with a huge impact. Everyone hears at school about the Black Death in the 1300s, yet here was an infectious disease only 85 years ago that killed 40 million people and for some reason we don’t know about it.”

At top, the preserved tissue samples Taubenberger is studying.

Taubenberger’s chief scientific interest, he says, is “basic immunology.” But the 1918 flu, he admits, is a “hobby that has kind of taken over my life.” His passion for understanding the virus began in large part because of circumstance. In 1983, Taubenberger left his previous job at the National Institutes of Health to take a position at the Armed Forces Institute of Pathology in Rockville, Maryland, to create a state-of-the-art molecular pathology laboratory. Traditionally, a pathologist will diagnose disease by examining tissue samples under a microscope to look for the distinctive cellular changes that mark a tumor cell, for example, and indicate that it is benign or malignant. “But molecular medicine has advanced so much that there are many conditions, including some tumors, that have particular genetic mutations associated with them, so you can make a diagnosis of cancer or leukemia by looking at the DNA for that particular mutation,” explains Taubenberger. “I was charged with setting up such a lab. As part of our work we developed techniques to recover nucleic acids” — the building blocks of our DNA strands — “from tissues that had been fixed in formaldehyde.” Although pathologists commonly study fixed tissues, molecular biologists prefer fresh blood and tissue samples because the preservation process can break up and damage DNA.

Taubenberger examines the results of some recent research.

Those techniques allowed him to take advantage of a unique database. The Armed Forces Institute of Pathology, where Taubenberger is now chief of the Division of Molecular Pathology, has been in existence for more than 140 years and houses a vast collection of preserved tissue specimens — including, Taubenberger discovered, samples from victims of the 1918 influenza outbreak. “At some point around 1996 it occurred to me that it would be useful to look at the 1918 flu through the lens of molecular biology. Here was something that we thought was very medically relevant, it was an outbreak that had killed tens of millions of people, and nobody knew anything about it because viruses weren’t even known then to be human pathogens,” he says.

Taubenberger’s studies have proven to be more than “relevant.” He and his colleagues are on the verge of determining the 1918 strain’s entire genetic code and they’ve shed light on the origin of the virus and why it was so peculiarly deadly to young adults. As part of the work, he and his team

reconstructed the genes of the virus and inserted them individually into other viruses. Taubenberger bristles at the assertion by some activist groups that recreating, at least in part, the deadly 1918 virus would be considered bioterrorism if the work were done outside of the United States: “I’ve seen references like that but I don’t think the claims are appropriate. These people have never contacted me. They make references to papers and draw conclusions that have nothing to do with the papers they are referencing, so they are not looking at the science carefully.”

“I think one thing these people get excited about is that the Armed Forces Institute of Pathology belongs to the Department of Defense,” he adds. “But this is not a DOD-funded project. It is a project of my lab, being funded by the NIH. The sequences we generate are put into GenBank” — a storehouse of genetic sequence data that is publicly available. “It is clearly not a secret project.”

Furthermore, Taubenberger says, “the experiments that involve reconstructing viruses that contain 1918 genes are done in high biological containment with appropriate biosafety oversight. We don’t want to be cavalier and say there is nothing to worry about, no risk. What we want to say is that we think that working with this virus, trying to understand what happened in 1918 using the sequence of the virus, is really important work.”

In 1918, a flu pandemic ripped through the global population with such speed and virulence that by the end of the following year an estimated 40 million people would be dead — four times the number of victims eventually claimed by the First World War. The flu’s impact was simultaneously felt in nearly every corner of the earth, from the battlefields of Europe and Northern Africa to remote Inuit villages in Alaska and the grasslands of New Zealand. The international medical community, lacking the expertise to deal with the virus (which it mistakenly believed to be a bacterium), found itself powerless to stop the contagion from spreading. Hospitals ran out of beds for their sick. Morgues spilled out onto the streets, the corpses stacked on the sidewalks like cordwood. And the war ensured that the cycle would continue. Troops from both sides of the conflict, dispatched back and forth across the globe, were serving as the unwitting carriers of a lethal disease. The carousel of death kept turning.

Where did this particular flu strain come from, and what made it so deadly? 85 years later, virologists and epidemiologists the world over are still hunting down the answers to those two critical questions. Their quest has been imbued with a sense of urgency; modern health experts are bracing themselves for the emergence of a flu strain similar to 1918’s, with many suggesting a similar pandemic will occur within the next decade. The recent SARS outbreak showed the ability of the World Health Organization to promulgate widespread awareness of a deadly virus, but in the words of British virologist John Oxford, SARS was no flu. “If it was influenza A,” he says, “we would [have been] dusting down our pandemic plans. One day, one awful day, those plans will have to be brought out.”

The cornerstone of those plans will likely be the findings of scientists like American pathologist Jeffery Taubenberger. In 1997, in the U.S. Armed Forces laboratory where he works, Taubenberger discovered what virologists had been coveting for decades — lung tissue from a 1918 flu victim that contained fragments of the undamaged virus. For the past six years, Taubenberger has worked to map the virus’ genetic code one gene at a time in an effort to unlock the secret of how it killed millions. He even recently introduced some of the 1918 flu’s genes into present-day live virus and injected the modified strain into lung tissue cells to better study the impact it has on its host. “If we can shed light on why the 1918 virus was so lethal and can understand the genetic basis of that, that information can be applied to the emergence of new influenza strains,” Taubenberger says. “I think it’s really crucial that we do that.” But will Taubenberger and his colleagues crack the entire code in time?

In 1918, scientists didn’t know that the culprit behind the carnage was a virus, a simple capsule filled with a few snips of genetic material that allow it to harness its host’s cellular machinery and make limitless copies of itself. In many ways, the 1918 bug — a variety of influenza A, the most common cause of flu in humans — was no different than any other influenza virus. Within the viral capsule are eight strands of RNA, which carry a total of just eight genes. Two of the genes produce the sugar-rich proteins hemagglutinin and neuraminidase, which stud the surface of the virus with knob-like protrusions. The virus gains entry into a host’s cells with the aid of these two proteins, which have a distinctive structure in every flu strain and are the target of both flu vaccines and the body’s immune response. To start the infection process, enzymes naturally present in the host cut the hemagglutinin protein into two pieces so that it can bind to a receptor on the cell’s surface. The virus is then enveloped, pulled into the cell, and eventually released and broken apart when the neuraminidase protein destroys the receptor that connects virus to cell.

The RNA strands move toward the cell nucleus. There, the cell reproduces each strand and creates new proteins that are then packaged into capsules and ultimately released from the cell to infect other cells. In humans, the influenza virus selectively attacks and destroys the cells that line the upper respiratory tract, bronchial tubes, and trachea. One to two days after infection, the symptoms appear: shaking chills, fatigue, muscle ache, listlessness, and high fever. Flu mortality rates typically linger around 0.1 percent (despite the widespread availability of flu vaccines and modern antiviral drugs, 36,000 people still die every year in the United States from complications of the flu); in the 1918 flu, the rate was twenty-five times higher, with deaths usually the result of secondary bacterial pneumonia or bronchitis. Many flu victims in 1918 displayed a distinctive dusky blue-gray pallor on their face, lips, and ears, called heliotrope cyanosis — a mark of a patient who is being suffocated to death by a buildup of fluid and cells in his lungs.

Since the original broadcast of this program, Taubenberger’s team has successfully created a genetic sequencing of the 1918 virus, resurrected the virus itself to study its effects on lung tissue, and this fall announced a striking similarity between the 1918 virus and today’s H5N1 avian flu virus. Their findings indicate that the 1918 virus originated as a bird flu, confirming the legitimacy of concerns about avian flu. The updated episode includes new material and interviews with Taubenberger that reflect these new findings.