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The Influenza Threat
Pandemic in the Making
By Scientific American
Scientific AmericanCopyright © 2013 Scientific American, a division of Nature America, Inc.
All rights reserved.
Pandemics: Why We Should Be Worried
Capturing a Killer Flu Virus
by Jeffery K. Taubenberger, Ann H. Reid, and Thomas G. Fanning
On September 7, 1918, at the height of World War I, a soldier at an army training camp outside Boston came to sick call with a high fever. Doctors diagnosed him with meningitis but changed their minds the next day when a dozen more soldiers were hospitalized with respiratory symptoms. Thirty-six new cases of this unknown illness appeared on the 16th. Incredibly, by September 23rd, 12,604 cases had been reported in the camp of 45,000 soldiers. By the end of the outbreak, one third of the camp's population would come down with this severe disease, and nearly 800 of them would die. The soldiers who perished often developed a bluish skin color and struggled horribly before succumbing to death by suffocation. Many died less than 48 hours after their symptoms appeared, and at autopsy their lungs were filled with fluid or blood.
Because this unusual suite of symptoms did not fit any known malady, a distinguished pathologist of the era, William Henry Welch, speculated that "this must be some new kind of infection or plague." Yet the disease was neither plague nor even new. It was just influenza. Still, this particularly virulent and infectious strain of the flu virus is thought to have killed as many as 40 million people around the world between 1918 and 1919.
This most lethal flu outbreak in modern history disappeared almost as quickly as it emerged, and its cause was long believed lost to time. No one had preserved samples of the pathogen for later study because influenza would not be identified as a virus until the 1930s. But thanks to incredible foresight by the U.S. Army Medical Museum, the persistence of a pathologist named Johan Hultin, and advances in genetic analysis of old tissue samples, we have been able to retrieve parts of the 1918 virus and study their features. Now, more than 80 years after the horrible natural disaster of 1918 — 1919, tissues recovered from a handful of victims are answering fundamental questions both about the nature of this pandemic strain and about the workings of influenza viruses in general.
The effort is not motivated merely by historical curiosity. Because influenza viruses continually evolve, new influenza strains continually threaten human populations. Pandemic human flu viruses have emerged twice since 1918 — in 1957 and 1968. And flu strains that usually infect only animals have also periodically caused disease in humans, as seen in the recent outbreak of avian influenza in Asia. Our two principal goals are determining what made the 1918 influenza so virulent, to guide development of influenza treatments and preventive measures, and establishing the origin of the pandemic virus, to better target possible sources of future pandemic strains.
Hunting the 1918 Virus
In many respects, the 1918 influenza pandemic was similar to others before it and since. Whenever a new flu strain emerges with features that have never been encountered by most people's immune systems, widespread flu outbreaks are likely. But certain unique characteristics of the 1918 pandemic have long remained enigmatic.
For instance, it was exceptional in both its breadth and depth. Outbreaks swept across Europe and North America, spreading as far as the Alaskan wilderness and the most remote islands of the Pacific. Ultimately, one third of the world's population may have been infected. The disease was also unusually severe, with death rates of 2.5 to 5 percent — up to 50 times the mortality seen in other influenza outbreaks.
By the fall of 1918 everyone in Europe was calling the disease the "Spanish" influenza, probably because neutral Spain did not impose the wartime censorship of news about the outbreak prevalent in combatant countries. The name stuck, although the first outbreaks, or spring wave, of the pandemic seemingly arose in and around military camps in the U.S. in March 1918. The second, main wave of the global pandemic occurred from September to November 1918, and in many places yet another severe wave of influenza hit in early 1919.
Antibiotics had yet to be discovered, and most of the people who died during the pandemic succumbed to pneumonia caused by opportunistic bacteria that infected those already weakened by the flu. But a subset of influenza victims died just days after the onset of their symptoms from a more severe viral pneumonia — caused by the flu itself — that left their lungs either massively hemorrhaged or filled with fluid. Furthermore, most deaths occurred among young adults between 15 and 35 years old, a group that rarely dies from influenza. Strikingly, people younger than 65 years accounted for more than 99 percent of all "excess" influenza deaths (those above normal annual averages) in 1918–1919.
Efforts to understand the cause of the 1918 pandemic and its unusual features began almost as soon as it was over, but the culprit virus itself remained hidden for nearly eight decades. In 1951 scientists from the University of Iowa, including a graduate student recently arrived from Sweden named Johan Hultin, went as far as the Seward Peninsula of Alaska seeking the 1918 strain. In November 1918 flu spread through an Inuit fishing village now called Brevig Mission in five days, killing 72 people — about 85 percent of the adult population. Their bodies had since been buried in permafrost, and the 1951 expedition members hoped to find the 1918 virus preserved in the victims' lungs. Unfortunately, all attempts to culture live influenza virus from these specimens were unsuccessful.
In 1995 our group initiated an attempt to find the 1918 virus using a different source of tissue: archival autopsy specimens stored at the Armed Forces Institute of Pathology (AFIP). For several years, we had been developing expertise in extracting fragile viral genetic material from damaged or decayed tissue for diagnostic purposes. In 1994, for instance, we were able to use our new techniques to help an AFIP marine mammal pathologist investigate a mass dolphin die-off that had been blamed on red tide. Although the available dolphin tissue samples were badly decayed, we extracted enough pieces of RNA from them to identify a new virus, similar to the one that causes canine distemper, which proved to be the real cause of the dolphin deaths. Soon we began to wonder if there were any older medical mysteries we might solve with our institute's resources.
A descendant of the U.S. Army Medical Museum founded in 1862, the AFIP has grown along with the medical specialty of pathology and now has a collection of three million specimens. When we realized that these included autopsy samples from 1918 flu victims, we decided to go after the pandemic virus. Our initial study examined 78 tissue samples from victims of the deadly fall wave of 1918, focusing on those with the severe lung damage characteristic of patients who died rapidly. Because the influenza virus normally clears the lungs just days after infection, we had the greatest chance of finding virus remnants in these victims.
The standard practice of the era was to preserve autopsy specimens in formaldehyde and then embed them in paraffin, so fishing out tiny genetic fragments of the virus from these 80-year-old "fixed" tissues pushed the very limits of the techniques we had developed. After an agonizing year of negative results, we found the first influenza-positive sample in 1996, a lung specimen from a soldier who died in September 1918 at Fort Jackson, S.C. We were able to determine the sequence of nucleotides in small fragments of five influenza genes from this sample.
But to confirm that the sequences belonged to the lethal 1918 virus, we kept looking for more positive cases and identified another one in 1997. This soldier also died in September 1918, at Camp Upton, N.Y. Having a second sample allowed us to confirm the gene sequences we had, but the tiny quantity of tissue remaining from these autopsies made us worry that we would never be able to generate a complete virus sequence.
A solution to our problem came from an unexpected source in 1997: Johan Hultin, by then a 73-year-old retired pathologist, had read about our initial results. He offered to return to Brevig Mission to try another exhumation of 1918 flu victims interred in permafrost. Forty-six years after his first attempt, with permission from the Brevig Mission Council, he obtained frozen lung biopsies of four flu victims. In one of these samples, from a woman of unknown age, we found influenza RNA that provided the key to sequencing the entire genome of the 1918 virus.
More recently, our group, in collaboration with British colleagues, has also been surveying autopsy tissue samples from 1918 influenza victims from the Royal London Hospital. We have been able to analyze flu virus genes from two of these cases and have found that they were nearly identical to the North American samples, confirming the rapid worldwide spread of a uniform virus. But what can the sequences tell us about the virulence and origin of the 1918 strain? Answering those questions requires a bit of background about how influenza viruses function and cause disease in different hosts.
Flu's Changing Face
Each of the three novel influenza strains that caused pandemics in the past 100 years belonged to the type A group of flu viruses. Flu comes in three main forms, designated A, B and C. The latter two infect only humans and have never caused pandemics. Type A influenza viruses, on the other hand, have been found to infect a wide variety of animals, including poultry, swine, horses, humans and other mammals. Aquatic birds, such as ducks, serve as the natural "reservoir" for all the known subtypes of influenza A, meaning that the virus infects the bird's gut without causing symptoms. But these wild avian strains can mutate over time or exchange genetic material with other influenza strains, producing novel viruses that are able to spread among mammals and domestic poultry.
The life cycle and genomic structure of influenza A virus allow it to evolve and exchange genes easily. The virus's genetic material consists of eight separate RNA segments encased in a lipid membrane studded with proteins. To reproduce, the virus binds to and then enters a living cell, where it commandeers cellular machinery, inducing it to manufacture new viral proteins and additional copies of viral RNA. These pieces then assemble themselves into new viruses that escape the host cell, proceeding to infect other cells. No proofreading mechanism ensures that the RNA copies are accurate, so mistakes leading to new mutations are common. What is more, should two different influenza virus strains infect the same cell, their RNA segments can mix freely there, producing progeny viruses that contain a combination of genes from both the original viruses. This "reassortment" of viral genes is an important mechanism for generating diverse new strains.
Different circulating influenza A viruses are identified by referring to two signature proteins on their surfaces. One is hemagglutinin (HA), which has at least 17 known variants, or subtypes. Another is neuraminidase (NA), which has nine subtypes. Exposure to these proteins produces distinctive antibodies in a host, thus the 1918 strain was the first to be named, "H1N1," based on antibodies found in the bloodstream of pandemic survivors. Indeed, less virulent descendants of H1N1 were the predominant circulating flu strains until 1957, when an H2N2 virus emerged, causing a pandemic. Since 1968, the H3N2 subtype, which provoked the pandemic that year, has predominated.
The HA and NA protein subtypes present on a given influenza A virus are more than just identifiers; they are essential for viral reproduction and are primary targets of an infected host's immune system. The HA molecule initiates infection by binding to receptors on the surface of certain host cells. These tend to be respiratory lining cells in mammals and intestinal lining cells in birds. The NA protein enables new virus copies to escape the host cell so they can go on to infect other cells.
After a host's first exposure to an HA subtype, antibodies will block receptor binding in the future and are thus very effective at preventing reinfection with the same strain. Yet flu viruses with HA subtypes that are new to humans periodically appear, most likely through reassortment with the extensive pool of influenza viruses infecting wild birds. Normally, influenza HAs that are adapted to avian hosts bind poorly to the cell- surface receptors prevalent in the human respiratory tract, so an avian virus's HA binding affinity must be somewhat modified before the virus can replicate and spread efficiently in humans. Until recently, existing evidence suggested that a wholly avian influenza virus probably could not directly infect humans, but 18 people were infected with an avian H5N1 influenza virus in Hong Kong in 1997, and six died.
Outbreaks of an even more pathogenic version of that H5N1 strain became widespread in Asian poultry in 2003 and 2004, and more than 30 people infected with this virus have died in Vietnam and Thailand.
The virulence of an influenza virus once it infects a host is determined by a complex set of factors, including how readily the virus enters different tissues, how quickly it replicates, and the violence of the host's immune response to the intruder. Thus, understanding exactly what made the 1918 pandemic influenza strain so infectious and so virulent could yield great insight into what makes any influenza strain more or less of a threat.
A Killer's Face
With the 1918 RNA we have retrieved, we have used the virus's own genes as recipes for manufacturing its component parts — essentially re-creating pieces of the killer virus itself. The first of these we were eager to examine was the hemagglutinin protein, to look for features that might explain the exceptional virulence of the 1918 strain.
We could see, for example, that the part of the 1918 HA that binds with a host cell is nearly identical to the binding site of a wholly avian influenza HA. In two of the 1918 isolates, this receptor-binding site differs from an avian form by only one amino acid building block. In the other three isolates, a second amino acid is also altered. These seemingly subtle mutations may represent the minimal change necessary to allow an avian-type HA to bind to mammalian-type receptors.
Excerpted from The Influenza Threat by Scientific American. Copyright © 2013 Scientific American, a division of Nature America, Inc.. Excerpted by permission of Scientific American.
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