Merck is the only company licensed in the United States to produce the individual mumps vaccine, as well as the MMRII and a newer shot called the MMRV or ProQuad, which also contains the chickenpox vaccine. That gives Merck an effective monopoly on the product line, which by our estimate has brought the company as much as $10 billion in business since 2000. The complaint conservatively estimates MMRII purchases by the Centers for Disease Control and Prevention at $750 million.

If tests showed the mumps vaccine is ineffective -- or far less so than promised -- the door would be opened to any number of adverse events for Merck, from federal regulators pulling the licenses for all of its mumps-vaccine-containing products, to intensified competition from other manufacturers if they became aware of the problem.

What’s more, weak efficacy could be triggering real-time, real-world health problems here and abroad, where a version of the MMRII is also used. Mumps outbreaks unexpectedly occurred in the United States in 2006 and in 2009-10, reflecting the three-year cycle in which younger children become exposed. A total of 6,500 cases were reported in a highly vaccinated population in the Midwest in 2006, according to the suit, and another 5,000 cases in 2009; in the years leading up to the first outbreak, the annual average had been 265 cases.

If that pattern holds true, another outbreak might be due as early as this summer.

Additionally, poor vaccine efficacy has the effect of pushing some cases of mumps to a later age, when mumps is a more dangerous disease that can induce sterility in males. One intriguing implication is that no vaccine at all might have been better than the one Merck currently produces.

The suit claims that as a result of the fraud, the U.S. government has been cheated out of millions of dollars paid by the CDC to buy the vaccine for its immunization program. It says the agency, and other government bodies, were wrongly deprived of the knowledge they needed to make proper use of taxpayer money and sound medical decisions. (The CDC predicted several years ago that mumps would be eradicated in the United States by 2010, an outcome predicated on the idea that the vaccine worked.)

The suit describes Merck’s allegedly no-holds-barred effort to protect its market position. “Merck set out to conduct testing of its mumps vaccine that would support its original efficacy finding. In performing this testing, Merck’s objective was to report efficacy of 95 percent or higher regardless of the vaccine’s true efficacy. The only way Merck could accomplish this was through manipulating its testing procedures and falsifying the test results. … Krahling and Wlochowski participated on the Merck team that conducted this testing and witnessed firsthand the fraud in which Merck engaged to reach its desired results. Merck internally referred to the testing as Protocol 007.”

The suit says testing began in 1999, led by Senior Investigator David Krah and his second-in-command, Mary Yagodich. Merck’s Executive Director of Vaccine Research, Alan Shaw, approved the testing methodology, the suit says. Krahling said he complained about the fraud to Emilio Emini, Vice President of Merck’s Vaccine Research Division, and brought “actual testing samples and plaque counting sheets to demonstrate to Emini the fraudulent data that Krah was directing. Emini agreed that Krah had falsified the data,” the suit said, but defended some aspects of the work.

“Emini promised to conduct an ‘internal audit’ of the mumps testing. … Emini ordered Krahling not to call the FDA. Immediately after the meeting [a Human Resources representative] approached Krahling and again threatened that he would be put in jail if he contacted the FDA.” Shortly thereafter, Krahling was transferred to another lab, and soon left the company; Wlochowski was also transferred and left the next year. (In 2005, Emini became Executive Vice President of Vaccine Research and Development at Wyeth Pharmaceuticals. He is now Senior Vice President and Chief Scientific Officer of Vaccine Research at Pfizer.)

The suit describes how Merck scientists allegedly engaged in a number of techniques in order to claim that the vaccine remained effective, from essentially testing the vaccine against itself – using the weakened vaccine virus rather than the more virulent “wild” type to which children are exposed in the real world -- to adding animal antibodies that increased potency in lab tests; to, when all else failed, simply changing the data accurately recorded by Krahling, Wlochowski, and other virologists.

While many of the details of the alleged fraud are technical, one internal Merck document clearly describes the nature of the mission, according to the suit. It was titled: “Objective: Identify a mumps neutralization assay format [testing procedure] that permits measurement of a greater than or equal to 95% seroconversion rate in MMRII vaccines.”

Merck responded Friday that the suit is “completely without merit” and said the company will “vigorously defend” itself – presumably by quickly filing a motion to have the suit dismissed. Merck pointedly noted that, to date, the U.S. Department of Justice has not joined the suit.

Under the federal whistleblower statute, anyone can bring a whistleblower suit alleging that a business they worked for defrauded the United States government and, by extension, taxpayers. Such a suit remains sealed while the company has a chance to review it, and Department of Justice (DOJ) attorneys decide whether to join as plaintiffs, throwing the government’s weight behind the whistleblower’s claim that it was defrauded.

In this case the DOJ did not reach its decision on whether to join as a plaintiff quickly or definitively. The lengthy period between the filing of the suit by Krah and Wlochowski, on April 27, 2010, and the department’s decision not to intervene for the time being, on April 27, 2012, required the DOJ to request multiple six-month extensions, according to the civil docket for the case, filed in the Eastern District of Pennsylvania. In its statement declining to intervene, the department asked that if either side wants to settle or dismiss the case, “the court solicit the written consent of the United States before ruling or granting its approval.”

The mumps component of the combination measles-mumps-rubella (MMR) vaccine has long been a source of controversy.  Merck was first to market in the category introducing a vaccine named MMR in 1971, using a strain of mumps taken from the throat of a Merck scientist’s daughter named “Jeryl Lynn.” (In 1979, Merck replaced the MMR’s rubella component due to safety concerns and named the reformulated vaccine MMRII). Starting in 1986, the first serious competitors to Merck’s vaccine began to emerge based on a different mumps component: the so-called Urabe strain, which was first licensed by Japan’s Biken Institute in 1979. Urabe-based vaccines were licensed in countries all over the world, including Canada, Japan, and the United Kingdom, to name just a few. For many years, however, Merck was able maintained its advantage in the category by outpacing the performance of Urabe-based MMR vaccines.

Merck’s main advantage came from its superior safety reputation. One of the most troublesome adverse events for MMR vaccines, aseptic meningitis, is a serious and potentially fatal side effect of vaccination. According to a major textbook on vaccines, “the Urabe strain has been linked with aseptic meningitis wherever adverse reactions have been studied.” By contrast, according to another review cited in the complaint, “aseptic meningitis, the Achilles heel of mumps vaccines, has never been documented to be caused by Jeryl Lynn.” In country after country, introduction of Urabe-based MMR vaccines have spawned outbreaks of aseptic meningitis and prompted withdrawal of the suspect MMR vaccine. In several of these cases, Merck’s MMRII has been the primary beneficiary.

Some researchers have argued, however, that the superior safety profile of MMRII comes at the expense of reduced efficacy. According to the authors above, “a mathematical model using the Urabe or Jeryl Lynn strains, suggested that … the greater apparent safety … associated with the Jeryl Lynn strain is offset by the potentially greater effectiveness associated with the Urabe strain.”

In light of these competitive threats to its highly successful MMRII franchise, it’s not surprising that asking Merck scientists to oversee testing of the efficacy of its own mumps vaccine would create a conflict of interest, not to mention an incentive to cheat on the test, if the underlying efficacy of the vaccine was weak.

The DOJ’s decision also points to another unavoidable but potentially troubling conflict of interest – the department is part of the same Executive Branch of government as the FDA and CDC. Under the Department of Health and Human Services, the FDA and CDC approve, recommend, and monitor vaccines, and they have repeatedly certified mumps-containing vaccines as effective. Allowing an alleged fraud to go on under their noses, involving a vaccine to which they are strongly committed, might not be something they would care to acknoweldge.

The fate of the lawsuit notwithstanding, serious new questions about children’s health are now in the public domain. It will be worth watching whether regulators or legislators here or abroad ask Merck for convincing, current evidence that the mumps vaccine is working as promised, and that the public's health remains protected.

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Dan Olmsted is Editor and Mark Blaxill is Editor at Large of AgeofAutism.com. They are co-authors of The Age of Autism – Mercury, Medicine, and a Man-made Epidemic, published in 2010 by Thomas Dunne Books.