http://www.theatlantic.com/doc/200911/brownlee-h1n1
by Shannon Brownlee and Jeanne Lenzer
...But what if everything we think we know about fighting influenza is wrong? What if flu vaccines do not protect people from dying—particularly the elderly, who account for 90 percent of deaths from seasonal flu? And what if the expensive antiviral drugs that the government has stockpiled over the past few years also have little, if any, power to reduce the number of people who die or are hospitalized? The U.S. government—with the support of leaders in the public-health and medical communities—has put its faith in the power of vaccines and antiviral drugs to limit the spread and lethality of swine flu. Other plans to contain the pandemic seem anemic by comparison. Yet some top flu researchers are deeply skeptical of both flu vaccines and antivirals. Like the engineers who warned for years about the levees of New Orleans, these experts caution that our defenses may be flawed, and quite possibly useless against a truly lethal flu. ...
... Today, seasonal flu is estimated to kill about 36,000 people in the United States each year, and half a million worldwide.

Yet the flu, in many important respects, remains mysterious. Determining how many deaths it really causes, or even who has it, is no simple matter. We think we have the flu anytime we fall ill with an ailment that brings on headache, malaise, fever, coughing, sneezing, and that achy feeling as if we’ve been sleeping on a bed of rocks, but researchers have found that at most half, and perhaps as few as 7 or 8 percent, of such cases are actually caused by an influenza virus in any given year. More than 200 known viruses and other pathogens can cause the suite of symptoms known as “influenza-like illness”; respiratory syncytial virus, bocavirus, coronavirus, and rhinovirus are just a few of the bugs that can make a person feel rotten. And depending on the season, in up to two-thirds of the cases of flu-like illness, no cause at all can be found.

Nobody knows precisely why we are much more likely to catch the flu in the winter months than at other times of the year. ... What is certain is that influenza viruses mutate with amazing speed, so each flu season sees slightly different genetic versions of the viruses that infected people the year before. Every year, the World Health Organization and the Centers for Disease Control and Prevention collect data from 94 nations on the flu viruses that circulated the previous year, and then make an educated guess about which viruses are likely to circulate in the coming fall. Based on that information, the U.S. Food and Drug Administration issues orders to manufacturers in February for a vaccine that includes the three most likely strains.

Every once in a while, however, a very different bug pops up and infects far more people than the normal seasonal flu variants do. It is these novel viruses that are responsible for pandemics, defined by the World Health Organization as events that occur when “a new influenza virus appears against which the human population has no immunity” and which can sweep around the world in a very short time. The worst flu pandemic in recorded history was the “Spanish flu” of 1918–19, at the end of World WarI. A third of the world’s population was infected, with at least 40million and perhaps as many as 100million people dying—more than were killed in World Wars I and II combined. (Some scholars suggest that one reason World WarI ended was that so many soldiers were sick or dying from flu.) Since then, two other flu pandemics have occurred, in 1957 and 1968, neither of which was particularly lethal.

In August, the President’s Council of Advisors on Science and Technology projected that this fall and winter, the swine flu, H1N1, could infect anywhere between one-third and one-half of the U.S. population and could kill as many as 90,000 Americans, two and a half times the number killed in a typical flu season. But precisely how deadly, or even how infectious, this year’s H1N1 pandemic will turn out to be won’t be known until it’s over. Most reports coming from the Southern Hemisphere in late August (the end of winter there) suggested that the swine flu is highly infectious, but not particularly lethal. For example, Australian officials estimated they would finish winter with under 1,000 swine flu deaths—fewer than the usual 1,500 to 3,000 from seasonal flu. Among those who have died in the U.S., about 70 percent were already suffering from congenital conditions like cerebral palsy or underlying illnesses such as cancer, asthma, or AIDS, which make people more vulnerable.

Public-health officials consider vaccine their most formidable defense against the pandemic—indeed, against any flu—and on the surface, their faith seems justified. Vaccines developed over the course of the 20th century slashed the death rates of nearly a dozen infectious diseases, such as smallpox and polio, and vaccination became one of medicine’s most potent weapons. Influenza virus was first identified in the 1930s, and by the mid-1940s, researchers had produced a vaccine that was given to soldiers in World WarII. The U.S. government got serious about promoting flu vaccine after the 1957 flu pandemic .... Today, flu vaccine is a staple of public-health policy; in a normal year, some 100 million Americans get vaccinated.

But while vaccines for, say, whooping cough and polio clearly and dramatically reduced death rates from those diseases, the impact of flu vaccine has been harder to determine. Flu comes and goes with the seasons, and often it does not kill people directly, but rather contributes to death by making the body more susceptible to secondary infections like pneumonia or bronchitis. For this reason, researchers studying the impact of flu vaccination typically look at deaths from all causes during flu season, and compare the vaccinated and unvaccinated populations.

Such comparisons have shown a dramatic difference in mortality between these two groups: study after study has found that people who get a flu shot in the fall are about half as likely to die that winter—from any cause—as people who do not. Get your flu shot each year, the literature suggests, and you will dramatically reduce your chance of dying during flu season.

Yet in the view of several vaccine skeptics, this claim is suspicious on its face. Influenza causes only a small minority of all deaths in the U.S., even among senior citizens, and even after adding in the deaths to which flu might have contributed indirectly. When researchers from the National Institute of Allergy and Infectious Diseases included all deaths from illnesses that flu aggravates, like lung disease or chronic heart failure, they found that flu accounts for, at most, 10 percent of winter deaths among the elderly. So how could flu vaccine possibly reduce total deaths by half? Tom Jefferson, a physician based in Rome and the head of the Vaccines Field at the Cochrane Collaboration, a highly respected international network of researchers who appraise medical evidence, says: “For a vaccine to reduce mortality by 50 percent and up to 90 percent in some studies means it has to prevent deaths not just from influenza, but also from falls, fires, heart disease, strokes, and car accidents. That’s not a vaccine, that’s a miracle.”

The estimate of 50 percent mortality reduction is based on “cohort studies,” which compare death rates in large groups, or cohorts, of people who choose to be vaccinated, against death rates in groups who don’t. But people who choose to be vaccinated may differ in many important respects from people who go unvaccinated—and those differences can influence the chance of death during flu season. Education, lifestyle, income, and many other “confounding” factors can come into play, and as a result, cohort studies are notoriously prone to bias. When researchers crunch the numbers, they typically try to factor out variables that could bias the results, but, as Jefferson remarks, “you can adjust for the confounders you know about, not for the ones you don’t,” and researchers can’t always anticipate what factors are likely to be important to whether a patient dies from flu. There is always the chance that they might miss some critical confounder that renders their results entirely wrong.

When Lisa Jackson, a physician and senior investigator with the Group Health Research Center, in Seattle, began wondering aloud to colleagues if maybe something was amiss with the estimate of 50 percent mortality reduction for people who get flu vaccine, the response she got sounded more like doctrine than science. “People told me, ‘No good can come of [asking] this,’” she says. ..

Nonetheless, in 2004, Jackson and three colleagues set out to determine whether the mortality difference between the vaccinated and the unvaccinated might be caused by a phenomenon known as the “healthy user effect.” They hypothesized that on average, people who get vaccinated are simply healthier than those who don’t, and thus less liable to die over the short term. People who don’t get vaccinated may be bedridden or otherwise too sick to go get a shot. They may also be more likely to succumb to flu or any other illness, because they are generally older and sicker. To test their thesis, Jackson and her colleagues combed through eight years of medical data on more than 72,000 people 65 and older. They looked at who got flu shots and who didn’t. Then they examined which group’s members were more likely to die of any cause when it was not flu season.

Jackson’s findings showed that outside of flu season, the baseline risk of death among people who did not get vaccinated was approximately 60 percent higher than among those who did, lending support to the hypothesis that on average, healthy people chose to get the vaccine, while the “frail elderly” didn’t or couldn’t. In fact, the healthy-user effect explained the entire benefit that other researchers were attributing to flu vaccine, suggesting that the vaccine itself might not reduce mortality at all. Jackson’s papers “are beautiful,” says Lone Simonsen, who is a professor of global health at George Washington University, in Washington, D.C., and an internationally recognized expert in influenza and vaccine epidemiology. “They are classic studies in epidemiology, they are so carefully done.”

The results were also so unexpected that many experts simply refused to believe them. Jackson’s papers were turned down for publication in the top-ranked medical journals. One flu expert who reviewed her studies for the Journal of the American Medical Association wrote, “To accept these results would be to say that the earth is flat!” When the papers were finally published in 2006, in the less prominent International Journal of Epidemiology, they were largely ignored by doctors and public-health officials. ...."