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Chris Shaw wasn’t always skeptical about vaccines. The neuroscientist at the University of British Columbia had his teenage son vaccinated with most of the recommended shots. But then he started studying some of the ingredients commonly found in vaccines.

What he discovered caused him to go cold turkey on all shots for his six-year-old daughter. And that includes the vaccine for the H1N1 flu.

“I am not convinced H1N1 is sufficiently hazardous to most people to risk the potential downside of the vaccine,” Shaw said over the phone from his office in the research pavilion at the Vancouver Coastal Health Authority.

Shaw isn’t an easily dismissed vaccine conspiracy theorist. He is a leading expert on amyotrophic lateral sclerosis (ALS, or Lou Gehrig’s disease) and Parkinson’s disease. While investigating unusually high rates of ALS and other neurological disorders among veterans who have Gulf War syndrome, he found evidence that the cause may have been aluminum salt, an ingredient in the cocktail of vaccines given to soldiers before deployment.

Although aluminum salt isn’t present in the H1N1 vaccine, Shaw’s discovery made him concerned about other vaccines, including the swine-flu shot. He isn’t alone in his thoughts.

Despite a full frontal assault of news about the dangers of the flu and the importance of vaccination, a survey in late October revealed that only 36 percent of Canadians said they would get the shot. Lack of trust in the vaccine was cited as the main reason for vaccine opposition. Another poll in November found that 65 percent of Canadians believe the media has overreacted to the threat of swine flu.

Even many health workers aren’t convinced. In two separate surveys, in the U.K. (Pulse) and Hong Kong (British Medical Journal), published in August, half of health-care professionals said they didn’t intend to get the vaccine.

Canadian health officials and some newspaper columnists have reacted by accusing vaccine opponents of being conspiracy mongers or just plain irresponsible.

Who is right? Is the cure really worse than the disease? Let’s look at some numbers.

First, the disease. Swine flu had killed 161 Canadians as of November 12. That works out to one death per 200,000 Canadians in the past six-and-a-half months. Over the same period of time, major cardiovascular diseases typically claim 240 times more Canadian lives (about 39,000), cancer claims 230 times more (37,000 deaths), pneumonia kills 18 times more (2,800), and accidental falls claim eight times more (1,260), according to calculations based on 2005 Statistics Canada figures.

H1N1 has about the same death rate as hernias. But we don’t see scary front-page headlines for months on end about hernias, pneumonia, or falling down.

“It’s really not causing—and is not going to cause and nowhere has caused—significant levels of illness or death,” Dr. Richard Schabas, Ontario’s former chief medical officer of health, told the CBC on November 12.

Schabas said H1N1 “has ultimately turned out to be, from a pandemic perspective, a dud”.

What about the vaccine? Is it safe? Despite the onslaught of confident pronouncements from health officials and doctors, Shaw says he hasn’t seen enough information on the safety of the vaccine. “If the science were there, we could make a rational decision. But it’s a coin toss.”

Looking for answers, Shaw turned to the 24-page product-information leaflet on the vaccine released by drug giant GlaxoSmithKline. Health Canada used this document in approving the shot.

The leaflet leaves Shaw cold. “You couldn’t turn this in as a master’s thesis anywhere I know of and get a passing grade,” he said, calling the leaflet a “shocking document”.

Shaw said the material lacks basic information. For example, there is no safety data at all for several groups of people—pregnant women, people aged over 60, kids aged 10 to 17, and children under three. For kids three to nine years old, there is only “very limited” data.

“Where is the safety data that the government used to license the vaccine?” Shaw asked.

Health Canada would not talk to the Straight, and the Public Health Agency of Canada did not respond to a request for an interview.

The H1N1 vaccine includes a component called an adjuvant—which is used to boost the drug’s effectiveness—that has raised a lot of questions.

GlaxoSmithKline says the adjuvant has been tested on 45,000 people worldwide and that clinical trials are now being done on children. In an e-mail, spokesperson Melanie Spoore said the company is planning 25 trials of its various H1N1 vaccines before November 2010.

She also said a different but closely related vaccine made by the company, for the H5N1 flu, includes the same adjuvant and “is generally well-tolerated and has an acceptable safety profile” in both kids and adults.

But Shaw has concerns about the company’s trial results for the H5N1 vaccine. The product leaflet mentions a study in which the company injected the vaccine into pregnant rats. It found “an increased incidence of fetal malformations” and “delayed neurobehavioural maturation”. Another study did not produce the same outcome.

But Shaw says the rat results deserve more study. “Anytime you observe such outcomes, it is a concern,” he said.

The leaflet also mentions a study on ferrets. The animals were given adjuvanted and nonadjuvanted H5N1 vaccines and then exposed to the flu. The ferrets that got the adjuvanted vaccine were protected by the vaccine. But those that got the nonadjuvanted vaccine all died.

This result could be a concern, Shaw said, because Canadian authorities are telling pregnant women to get the nonadjuvanted H1N1 vaccine since the adjuvanted version hasn’t ever been tested on pregnant women. Shaw also said the animal-study information in the leaflet lacks many important details and would be “unpublishable” as presented. “Any [medical-journal] referee would kick this out the window.”

The company’s leaflet also paints a picture of the vaccine’s side effects in humans somewhat different than the usual line from health authorities. The Public Health Agency of Canada says on its Web site that the adjuvanted vaccine is as safe as the nonadjuvanted shot. It also says the rate of “serious adverse events” from vaccination is extremely low—typically “about one for every 100,000 doses of vaccine”.

What we don’t often hear is that the adjuvanted vaccine caused dramatically more side effects than the nonadjuvanted version. Ninety percent of 62 subjects reported pain (versus 37 percent of 62 people for the nonadjuvanted vaccine), 34 percent had muscle soreness (compared to 8 percent with the nonadjuvanted shot), and 14 percent experienced a headache (as opposed to 8 percent for the nonadjuvanted shot), according to the product-information sheet.

Although these reactions are minor, the leaflet also says four of 253 people studied experienced “severe adverse reactions”. Three of the four were deemed to be unrelated to the vaccine, but one case of hypersensitivity (which can mean anything from an allergic reaction to autoimmune disease) was determined “to be related to vaccination”.

That one serious reaction might not sound like a lot, but it actually translates into a rate of 395 cases per 100,000 people. That’s more than 50 times the rate of hospitalization due to H1N1 itself: 7.3 per 100,000 Canadians.

Sucharit Bhakdi is concerned some serious vaccine reactions could go unnoticed. He is a professor of medical microbiology at the Johannes Gutenberg University of Mainz in Germany. In October—in a coauthored paper in the journal Medical Microbiology—he warned of a possible increase in the risk in heart problems due to mass H1N1 vaccination.

Speaking by phone from his office, Bhakdi cited the higher rate of heart problems when 1.4 million U.S. soldiers were vaccinated for smallpox before the 2003 Iraq war.

Soldiers who received the vaccine had almost 7.5 times the rate of heart inflammation of nonvaccinated personnel, according to a study by U.S. military medical researchers in 2004 in the American Journal of Epidemiology.

“Unexpected serious adverse effects thus may follow in the wake of a general vaccination program,” Bhakdi’s paper said.

Yet health authorities and doctors are urging people with heart problems to get the H1N1 vaccine on a priority basis and do not appear to be monitoring them for possibly elevated risks, he said.

Shaw is also concerned about Canada’s monitoring of the side effects of vaccinations, calling the system “flimsy”.

What especially worries Shaw is the possibility of longer-term side effects from the vaccine. Most vaccine safety studies monitor patients for a few days or, at most, several months.

That isn’t enough, Shaw says. With some vaccines, the most serious reactions have taken years to surface. “Neurological problems don’t happen overnight,” he said. “It took five to 10 years to see the bulk of the Gulf War–syndrome outcomes.”

One of the best examples involves a controversial ingredient present in the H1N1 vaccine: thimerosal. Thimerosal is a form of mercury used in some vaccines as a preservative. Drug makers agreed to phase it out of most vaccines after the U.S. Food and Drug Administration found in 1999 that mercury levels in children who had gotten multiple shots often exceeded safety levels set by the Environmental Protection Agency (EPA). Nonetheless, thimerosal still remains in many flu vaccines.

Controversy has raged for years about whether or not thimerosal is behind soaring childhood autism rates. While that debate continues, a 2008 study in the U.K. journal Toxicological and Environmental Chemistry found that boys who were given a vaccine containing thimerosal were nine times more likely to have developmental problems than unvaccinated boys.

The Public Health Agency of Canada says on its Web site that thimerosal is safe and that the amount in the H1N1 vaccine is below Health Canada’s daily safety limit set for mercury. “There’s significantly less mercury in the vaccine than you would find in a can of tuna fish,” the site states.

In fact, the amount of mercury in the nonadjuvanted H1N1 vaccine does actually exceed the daily safety level for pregnant women. Health Canada has established the safe dietary level of mercury for pregnant women at 0.2 micrograms (millionths of a gram) per kilo of body weight. The nonadjuvanted H1N1 vaccine contains 25 micrograms of mercury.

Simple math tells us an average Canadian pregnant woman—weighing 80 kilograms at term—gets about 56 percent more than the daily safe level of mercury when given a dose of the nonadjuvanted vaccine. By the EPA’s stricter standards, that same dose is actually triple its daily safe level.

What’s more, Shaw notes, those daily safety levels were set for consumption of mercury in food, not for injection directly into the body. Injecting a neurotoxin like mercury has much more impact than eating it, he said.

Squalene is another controversial component of the swine-flu vaccine. It’s an oil found in animal livers and is used as an adjuvant in vaccines and also as a moisturizer in cosmetic products. It is primarily gotten from shark livers—a fact that has upset conservation groups worried about endangered shark populations. Some companies, like Unilever and L’Oréal, have agreed to stop using squalene in cosmetic products.

Debate has raged for years about whether or not squalene is responsible for Gulf War syndrome. Most research suggests that’s not the case, but in recent years much more solid evidence has found squalene can cause autoimmune diseases like lupus and rheumatoid arthritis in animals.

Still other questions have been raised about polysorbate 80, another component of the H1N1 vaccine adjuvant. Studies have found it can cause severe allergic reactions and hypersensitivity.

In the end, we might only get a good picture of the vaccine’s side effects long after swine flu has run its course. Then again, with Canada’s lax monitoring system for side effects, we may never know which was worse.