Pandemic influenza awareness week. Day 2: Our adventures with avian flu

Anyone working in the area of influenza virus epidemiology is familiar with the name Robert Webster. A virologist at St. Jude’s Children’s Hospital in Memphis, the native New Zealander has been leading the charge against influenza for well over 40 years. Barely out of graduate school, Webster hypothesized that something like genetic reassortment (which had not yet been discovered) occurred to cause the big changes that appeared among human influenza viruses, driving pandemics. He performed a simple experiment that cemented the course of his career: he found that serum from patients who had survived the 1957 influenza pandemic reacted with avian influenza viruses. Later genetic analyses showed that the “Asian flu” virus had indeed received 3 of its 8 gene segments from birds. It happened again in 1968: the pandemic virus was the result of a reassortment between human and avian influenza viruses. These observations led to more than 30 years of surveillance of waterfowl in many different countries, and the revelation that these waterfowl constitute a reservoir of all known subtypes of influenza virus.

Webster’s worst fears seemed to be coming true in 1997. Hong Kong was experiencing an influenza outbreak in chickens so severe it had been nicknamed “chicken Ebola.” Humans were also affected. The first case was in a 3-year-old boy from Hong Kong. Though doctors knew he had died of the flu, they were uncertain of the strain, and sent samples off to several high-level laboratories for further testing. When it came back H5N1, the Centers for Disease Control and Prevention sent Keiji Fukuda to Hong Kong to investigate. After a month of searching, he and his team found no further evidence of infection with this avian virus in the human population–so they left, writing off the boy’s illness as a “freak occurrence.” They were premature. By the end of the year, 18 cases had been confirmed; 6 died. Clinical features often included a primary viral pneumonia and death quickly after onset of symptoms. The route of transmission in all cases appeared to be direct bird-to-human contact. Fearing a public health crisis, officials ordered the culling of Hong Kong’s entire poultry population. Analysis of the virus showed it to be a serotype H5N1 virus.

Though H5N1 has gotten the lion’s share of the spotlight, other avian viruses have caused human disease in the past decade. In The Netherlands, an H7N7 virus caused 89 infections with 1 death in 2003. Human infections with avian H7N3 were reported in British Columbia in 2004, and with H7N1 and H7N3 in Italy between 1999 and 2003. Avian H9N2 viruses were in the spotlight in 1999, when they were found in 3 children in Hong Kong who were suffering from flu-like symptoms. All three recovered.

The United States isn’t isolated from this type of outbreak, either. During 1983 in Pennsylvania, influenza burned through the poultry population, where health officials there resorted to the same drastic measure they took in Hong Kong: destruction of the entire poultry stock. In 2002, avian H7N2 caused an outbreak among poultry in Virginia, and at least one serologically-confirmed human case. This virus was seen again in the United States in 2003, when a patient showed up at a New York hospital with respiratory symptoms. It’s still unknown how he contracted the virus.

Clearly, avian viruses infect humans periodically–quite likely, much more often than we know about. However, H5N1 seems to be different. It has infected, and killed, an incredibly diverse group of animals, including those who normally are unaffected by influenza: blue pheasants, black swans, turtledoves, leopards, mice, domestic cats, even tigers. And both laboratory and clinical analyses conclude that it seems to have gotten worse since 1997.

H5N1 was back on the radar in 2003, when it caused 35 cases (24 of them fatal) in Vietnam and Thailand. In 2004, the virus caused 44 known cases in humans; 32 of them were fatal. Most of these cases were in previously-healthy children and adults. Poultry was again infected, and this time around seemed to be even more virulent. 120 million birds were killed between January and March of 2004. Additionally, pigs had been infected. This was particularly worrisome, as pigs had long been thought to act as a “mixing vessel” between human and avian strains. (Pig cells are able to bind both human and avian hemagglutinin; thus, viruses of both types can replicate within their cells, with the possibility of recombination and spread of a “humanized” avian virus). Animals normally resistant to influenza disease were again affected. Leopards and tigers died in a Thai zoo after consuming infected raw chicken. In the latter case, it seems that tiger-to-tiger transmission occurred as well.

There is also evidence for at least one case of human-to-human transmission during this outbreak. In Thailand, a young girl died, followed shortly by her mother, who had served as her nursemaid. No contact between the mother and poultry could be found. Additionally, an aunt of the girl, who had also assisted in her care, complained of a sore throat, cough, and fever. She was later found to be infected with H5N1 as well. It was feared that this could be the beginning of The Big One. However, no other cases stemmed from these, and it seems likely that the transmission was due to the large amount of time spent in close contact with the girl and her secretions; the virus did not appear to be easily passed person to person–so far.

As of October 2005, cases of avian H5N1 have been reported in Thailand, Cambodia, Indonesia, and Vietnam. Combined, there have been 72 cases and 28 deaths in these countries since the end of 2004, and a total of 116 confirmed cases and 60 deaths since 2003. These are likely underestimates. If anything can be said about H5N1, it’s that it is unpredictable. A case was written up in the February 2005 New England Journal of Medicine detailing a fatal case where a child presented with severe diarrhea, followed by seizures, coma, and death. A sibling had died of the same symptoms two weeks earlier, and neither child showed any respiratory symptoms characteristic of influenza. Nevertheless, H5N1 virus was isolated from several specimens isolated from the second patient. Therefore, we are likely missing even many symptomatic infections–because they are presenting with the wrong symptoms. It is worrisome to think that the virus may be adapting to humans during infections like these. Additionally, avian influenza has been shown to cause asyptomatic infections. A report in the October Journal of Infectious Diseases showed that in a group of workers exposed to avian H7N1 and H7N3 influenza viruses during the Italian outbreak of 1999-2003, 7 of 183 people tested were seropositive to at least one of the viruses, suggesting they had been infected during the epidemic. None reported a history of influenza-like illness following exposure to the avian viruses. It’s not known what the extent of sub-clinical infection with these viruses may be, either in Asia, or in the United States or Europe.

An influenza pandemic is a kind of viral perfect storm. Three requirements must be met: 1) the human population must lack antibodies to the virus; 2) the virus must make humans ill; 3) the virus must be efficiently transmitted between humans. H5N1 certainly meets the first two requirements; the scientific community is holding its collective breath waiting for the third condition to be met. In tomorrow’s article, I’ll discuss more about surveillance efforts and models used to predict or control an outbreak, should one occur.

Robert Webster is currently in his mid-seventies, and much of that life has been spent battling and studying influenza. With all he’s seen, it’s significant that he’s made the following comments regarding H5N1:

This is the worst flu virus I have ever seen or worked with or read about. We have to prepare as if we were going to war–and the public needs to understand that clearly. This virus is playing its role as a natural bioterrorist. The politicians are going to say Chicken Little is at it again. And, if I’m wrong, then thank God. But if it does happen, and I fully expect that it will, there will be no place for any of us to hide. Not in the United States or in Europe or in a bunker somewhere. The virus is a very promiscuous and efficient killer.

This is the “war on terrorism” that we really should be sinking money into. Even if H5N1 isn’t the next pandemic strain, or if it is but doesn’t come anywhere near the level of the 1918 outbreak, it has served to point out holes in our preparation procedures for a disaster of that magnitude. More on that tomorrow.

Other posts in the series:
Day 1: History of Pandemic Influenza.

More resources on pandemic influenza:

  • CIDRAP Pandemic influenza news
  • Infectious Disease Society of America (IDSA) Pandemic/Avian flu
  • CDC’s site on Avian flu
  • Flu wiki
  • Pandemic influenza awareness week. Day 1: History of pandemic influenza

    It’s hard to avoid hearing about influenza virus these days. In all the noise, it’s tough to sort out the facts from the rumors and conspiracy theories. I’ve already discussed a bit about the basic biology of the virus in this post, so I’m not going to review that here (though a good overview can be found here for those of you who need to bone up on your influenza virus biology). So, this week, as a part of Pandemic influenza awareness week, I’ll be writing a 5-part series about various issues regarding influenza. Today, I’ll discuss the history of influenza, focusing on past pandemics. The rest of the week will address the following topics, with the goal of presenting a review of the facts without the scare-mongering:

  • “Avian flu” and H5N1, 1997-present
  • How do we prevent/control a pandemic? What models and surveillance can tell us
  • Where we are now–are we ready for a pandemic?
  • Other issues in influenza

  • So, without further ado, let’s dive into today’s topic:

    A quick trip through the history of pandemic influenza

    Influenza is an ancient disease. It is first described by Hippocrates in 412 BC, though the term “influenza” would not be coined until the 14th century. (“Influenza” is Italian for “influence,” as the prevailing idea of disease causation at that time was the influence of the stars). In 1580, a disease originating from Asia and thought to be influenza swept through Europe, Africa, and the Americas on trade routes. While these cannot be confirmed as influenza, a better handle on the symptoms of the disease makes it likely that several influenza pandemics occurred in the 1800s: in 1833, 1836, 1847 and 1889.

    The worst influenza pandemic in recorded history took place in 1918-1919. At least 40 million, and likely closer to 100 million deaths worldwide have been attributed to the virus, most of them occurring in the 16-week period between September-December 1918. In large U.S cities, more than 10,000 deaths per week were attributed to the virus. It is estimated that as many as 50% of the population was infected, and ~1% died. To compare, in “normal” (interpandemic) years, it is estimated that between 10-20% of the population is infected, with a .008% mortality.

    Despite its popular name of the “Spanish flu,” it’s uncertain where the pandemic originated. (During World War I, Spain was one of the few countries who did not censor media, so reports of the state of the epidemic in that country were widely circulated). Scientists and historians have put forth points of origin in China, Vietnam, India, France, Great Britain, and the U.S. (Kansas). Contemporary reports of the pandemic contain imagery that harkens back to the 14th century Black Plague. Morgues were overwhelmed; dead were buried in simple pine boxes, as the supply of caskets was quickly depleted; public activities were cancelled; spitting on the street was criminalized. The death toll made the casualties as a result of World War I pale by comparison. The virus struck hardest in the young and healthy, whose rapid immune response actually became their downfall. Enough young people died that it dramatically decreased the average life expectancy in that year (see figure below, from Nature Medicine 10, S82 – S87 (2004)).

    Typically, influenza causes death due to a secondary bacterial pneumonia. Bacteria are able to take advantage of the host’s compromised immune status and damaged lung cells, establishing a potentially deadly infection. However, during the 1918 pandemic, a greater percentage of the deaths in the 20-45 age group were due to primary pneumonia: pneumonia caused by a combination of the influenza virus and the host response, with no bacterial invaders involved. In some patients, this occurred within a matter of hours from the first symptoms. A Pennsylvania medical student documented the phenomenon:

    As their lungs filled, the patients became short of breath and increasingly cyanotic. After gasping for several hours, they became delirious and incontinent, and many died struggling to clear their airways of a blood-tinged froth that sometimes gushed from their nose and mouth. It was a dreadful business.

    Though serological studies carried out in the 1930s had already identified the virus as a serotype H1N1, it was long thought that was the end of the potential information that could be found about the virus. However, in the mid-1990s, a group of researchers led by Jeffrey Taubenberger at the Armed Forces Institute of Pathology found samples of lung tissue from soldiers who had died of the 1918 virus in the archive at that institute. Additionally, pathologist Johan Hultin provided an additional sample from the lungs of an Inuit woman in Alaska who had died during the pandemic. These samples have been sequenced in an effort to determine what it was that made the 1918 virus so virulent. Though these questions are still being investigated, the preliminary data suggests that the virus was a human-avian reassortant which had entered the human population a short time before the pandemic (likely 6-12 months).

    Though the 1918 pandemic has been the most dramatic example of the killing potential of influenza, there have been 2 other pandemics in the last 100 years. In 1957, a H2N2 virus appeared in China. This “Asian flu” quickly swept through the population, replacing the previously-circulating H1N1 virus and killing 70,000 in the U.S. Similarly, in 1968, an H3N2 virus emerged from Hong Kong to replace the H2N2 virus. This pandemic resulted in 34,000 American deaths. The H1N1 serotype re-surfaced in 1977, and currently, H3N2, H1N1, and reassortant H1N2 viruses circulate in the human population.

    The H1N1 caused an additional scare in 1976. In January of that year, a private at Fort Dix, New Jersey, collapsed and died following a march. It was determined that he died of “swine flu,” serotype H1N1. Although he was the only death at the fort, health officials were highly concerned. Secretary of health F. David Matthews stated that

    there is evidence there will be a major flu epidemic this coming fall. The indication is that we will see a return of the 1918 flu virus that is the most virulent form of flu. In 1918, half a million people died. The projections are that this virus will kill one million Americans in 1976.

    With hindsight, we can see that a proclamation with this level of certainty is folly, but at the time, it was thought that influenza cycled in a fairly regular pattern, varying between very high pathogenicity strains and lower pathogenicity strains. It was thought that the world was overdue for another high pathogenicity strain, and that the “swine flu” virus just might be the one. In March of 1976, President Ford announced that he would ask Congress for funds to produce enough vaccine “to inoculate every man, woman, and child in the United States.” Of course, this epidemic never materialized, and actually dealt a blow to the influenza vaccine campaign, as reported side effects of the vaccine included Guillain-Barré syndrome, a debilitating neurologic condition.

    Looking back, one can certainly draw parallels between the scare and build-up to vaccination in 1976 and today with H5N1. However, just because that pandemic never materialized does not mean that the same thing will happen with today’s “avian flu.” At this point, we just don’t know, but it behooves us to hope for the best, but prepare for the worst.

    Tomorrow: all about avian flu and H5N1, from its initial identification in 1997 to today.

    More resources on pandemic influenza:

  • CIDRAP Pandemic influenza news
  • Infectious Disease Society of America (IDSA) Pandemic/Avian flu
  • CDC’s site on Avian flu
  • Flu wiki
  • Marshall and Warren win prize for work on Helicobacter as cause of peptic ulcers

    But I thought biologists were too “close-minded?”

    Australians Barry J. Marshall and Robin Warren won the 2005 Nobel Prize in medicine Monday for showing that bacterial infection, not stress, was to blame for painful ulcers in the stomach and intestine.

    The Australians’ idea was “very much against prevailing knowledge and dogma because it was thought that peptic ulcer disease was the result of stress and lifestyle,” Staffan Normark, a member of the Nobel Assembly at the Karolinska institute, said at a news conference.

    This is a great example of how science works. These men proposed a hypothesis that was pretty far outside the mainstream at the time (even though there had been some antecdotal and published evidence regarding antibiotic treatment and resolution of ulcers). They tested it; they gathered evidence to support it; they published their results in the literature; and eventually, they overturned the prevailing notion that ulcers were caused by stress and diet based on the experimental evidence. They didn’t rely on think tanks, or mission statements, or pressure from supporters in high places in order to have their ideas accepted–they won over their audience on the merits of their research. Was it easy? From interviews I’ve read, hell no. But they perservered, others joined them in uncovering evidence that supported their hypothesis, and today, they’ve been rewarded with one of the highest honors that a scientist can receive. Congratulations, gentlemen, and let this serve as yet another example of scientists embracing new ideas when they’re backed by quality research.

    Hurricane victims face new microbial threat: mold

    As if it wasn’t bad enough already…

    Mold now forms an interior version of kudzu in the soggy South, posing health dangers that will make many homes tear-downs and will force schools and hospitals to do expensive repairs.

    It’s a problem that any homeowner who has ever had a flooded basement or a leaky roof has faced. But the magnitude of this problem leaves many storm victims prey to unscrupulous or incompetent remediators. Home test kits for mold, for example, are worthless, experts say.

    Don’t expect help from insurance companies, either. Most policies were revised in the last decade to exclude mold damage because of “sick building” lawsuits alleging illnesses. Although mold’s danger to those with asthma or allergies is real, there’s little or no science behind other claims, and a lot of hype.

    Even for those whose homes were spared the worst of the devastation, the mold problem might be too great for them to be habitable again. As anyone who’s dealt with mold clean-up knows, it’s a huge pain in the ass, and if you miss just a little bit it can come back with a vengeance.

    Emergence of canine influenza

    Canine flu strikes in Westchester county, NY.

    A NEW strain of influenza that began infecting dogs in Florida early last year has recently struck hard in the Westchester area, forcing the temporary closure of two kennels after more than 100 dogs being boarded there became ill, veterinary officials say.

    Gracelane Kennels in Ossining underwent decontamination after a viral illness infected dogs. Eddie Loga hoses down a run at the kennel. Although prepared for the less-virulent kennel cough, boarding sites have been blindsided by the new virus.

    At least one of the dogs has since died. The two sites, Gracelane Kennels in Ossining and a branch of Best Friends Pet Care in Chestnut Ridge in Rockland County, have undergone decontamination procedures.

    The symptoms mimic those of bordetella, a less virulent illness commonly known as kennel cough, for which all dogs must be vaccinated before they are boarded. Health officials fear that this similarity has contributed to underreporting of the spread of the new illness, both locally and nationally.

    There is not yet any vaccine for the new virus, which is believed to have jumped from horses to dogs last year.

    This once again shows how badly we need good surveillance for zoonotic diseases. Here we have an influenza strain that’s already jumped species, is likely causing more illness than is being attributed to it, and has been shown to be potentially lethal in the new population. I’ve no doubt that similar events are happening all the time, and we’re missing them–and therefore, missing chances to intervene before they become established in the new population. But I guess, why pay for public health funding, when there’s wars to be fought?

    Edited to add: Previous article.

    The virus, which scientists say mutated from an influenza strain that affects horses, has killed racing greyhounds in seven states and has been found in shelters and pet shops in many places, including the New York suburbs, though the extent of its spread is unknown.

    How many dogs die from the virus is unclear, but scientists said the fatality rate is more than 1 percent and could be as high as 10 percent among puppies and older dogs.

    They say it’s killed greyhounds in Iowa as well…first I’ve heard of it. Which again underscores that folks in veterinary public health need to be in better touch with those of us in human public health as well.

    Dobzhansky and anthrax

    The Washington Post today reminds us that there has been little progress in uncovering the source of the 2001 anthrax attacks. [1]

    First, a disclaimer. I’m not an “evolutionary biologist,” per se. I have what is I swear the longest job title ever–molecular infectious disease epidemiologist. As such, I often get asked, “what’s the relevance of evolution to your work?” Or, I’ll read editorials such as Dr. Skell’s recently in The Scientist [2] questioning the use of evolutionary theory in experimental biology, and be disheartened. Yet the method of investigating the anthrax attacks shows once again just how relevant evolutionary theory is to all areas of biology, and how Dobzhansky’s famous “Nothing makes sense…” comment once again ring true.

    There are several clues regarding the 2001 attack (for those unfamiliar with the story, the background can be found here) [3]. Some are in the packaging of the material: the writing on the envelope, the location of the postmark, the mailbox where the letters were dropped. Others are in the processing of the anthrax: the spores were finely milled, so as to be more easily aerosolized. Finally, there are clues in the bacteria themselves: in their genetic makeup. Early on, they looked at the molecular profiles of the anthrax and compared them to known strains, zeroing in on the Ames anthrax strain.

    This is a good thing, because the Ames strain is fairly rare in nature–making it more likely that the anthrax was obtained from a laboratory. The problem with anthrax, however, is that as a species, it is very homogeneous: there isn’t a lot of variation in the DNA sequence. Fingerprinting techniques like pulse field gel electrophoresis (PFGE), which uses restriction enzymes to cut the bacterial chromosome into smaller pieces to be run out on agarose gels, work well for pathogens like E. coli and Staphylococcus aureus, but isn’t nearly as useful in anthrax due to the low level of sequence diversity. This makes it necessary to use more sensitive techniques to identify the bacterium, bringing us back to the characterization of the 2001 bioterrorist strain as the Ames anthrax strain.

    What is the “Ames strain,” exactly? In a 2001 Science article [4], it was noted that

    Over the past 2 decades, the U.S. Army Medical Research Institute of Infectious Diseases [USAMRIID] in Fort Detrick, Maryland, sent the Ames strain to several research labs. And as it was passed around and grown in different labs, it may well have accumulated minute new changes.

    Researcher Martin Hugh-Jones noted, “The Ames strain can be many different things. A very detailed fingerprint could reveal very very minor variations.”

    Therefore, it’s the accumulation of these mutations–from a common ancestor, the original “Ames strain” (sound familiar?)–that may allow for a more specific determination of the origin of the 2001 strain, shedding light on the most notable biocrime in recent history. I’ve not seen a published comparison of the whole genome sequences of the various Ames strains, but that seems like the logical way to proceed in this (apparently stalled) investigation–go right back to that “useless” evolutionary biology to save the day.


    [1] Lengel, A. “Little progress in FBI probe of anthrax attacks.” Washington Post. September 16, 2005.
    [2] Skell, PS. 2005. “Why do we invoke Darwin? Evolutionary theory contributes little to experimental biology.” The Scientist. 19:10.
    [4] Enserink, M. 2001. “Taking anthrax’s genetic fingerprints.” Science: 294; 1810-2.

    Plaque–evidence for Design!

    Every now and then, I check in over at The Institute for Genomic Research (TIGR) to see what new projects they’re up to, as well as to see if they’ve released a particular genome sequence I’m waiting on. Yesterday I noticed this project:

    Innovative Metagenomics Strategy Used To Study Oral Microbes

    Rockville, MD – The mouth is awash in microbes, but scientists so far have merely scratched the surface in identifying and studying the hundreds of bacteria that live in biofilm communities that stick to the teeth and gums.

    In an innovative new project that could help improve the detection and treatment of oral diseases, scientists are now using a metagenomics strategy to analyze the complex and difficult-to-study community of microbes in the oral cavity.


    In recent years, molecular methods have indicated that there are well over 400 species of bacteria in the oral cavity. But, so far, only about 150 of those species have been cultured in laboratories and given scientific names. Using a metagenomics sequencing strategy, TIGR scientists will be able to identify bits and pieces of the DNA of many of those oral microbes that so far have not been grown in labs and studied.

    Now, I know that there are an insane amount of microbes in the mouth, but 400 species Holy cow.
    Continue reading “Plaque–evidence for Design!”