The story begins in December 2020, when the US Centers for Disease Control and Prevention prepared to roll out the first mRNA covid-19 vaccines. Before the first doses were administered, the CDC assured healthcare professionals and the public that the Vaccine Adverse Event Reporting System, or VAERS, could quickly identify potentially harmful reactions following vaccination. VAERS, a long-standing national early-warning system operated jointly by the CDC and the Food and Drug Administration, depends on voluntary reports from clinicians, vaccine manufacturers, and members of the public, and it was intended to serve as the first line of defense in spotting unexpected patterns of harm.

To mine that flood of incoming reports for danger signals, the CDC planned to deploy two complementary data-mining techniques. The first was the proportional reporting ratio, or PRR, a statistical measure that compares how often a particular adverse event appears in reports for a given vaccine against how often it appears for all other vaccines in the database. The second was an empirical Bayesian method supplied by the FDA, which uses prior expectations to determine whether observed reporting frequencies are unusually elevated. According to the original plan, the two agencies would run both methods, share their results, and discuss any discrepancies. That plan, the investigation found, was quietly abandoned.

In a letter cited by The BMJ, then CDC Director Rochelle Walensky acknowledged that the agency did not perform PRR analyses until 2022, more than a year after the vaccines had been given to hundreds of millions of Americans. In the interim, both the CDC and the FDA chose to rely entirely on the FDA’s Bayesian method. That decision would prove consequential, because the FDA’s algorithm carried a structural flaw that, according to internal records, agency officials understood before the pandemic even began: it was effectively blind to adverse events that were elevated by both major mRNA vaccines at the same time.

The technical reason for this blindness lies in the mathematics of disproportionality analysis. By early 2021, more than 90 percent of all VAERS reports concerned the new mRNA vaccines made by Pfizer and Moderna. If both vaccines raised the risk of an adverse event, such as myocarditis, in roughly equal amounts, then the observed frequency of that event in the database would closely match the expected frequency calculated against the background of all other vaccines. The two values would cancel each other out, and no automated alert would ever fire. In other words, the very dominance of the new vaccines in the reporting stream neutralized the statistical machinery designed to detect harm.

Internal government documents show that FDA officials were aware of this limitation before and during the pandemic, and that CDC officials were informed of the problem while the vaccination campaign was underway. In early 2021, FDA medical officer Dr Ana Szarfman, working with statistician William DuMouchel, the original developer of the Bayesian algorithm, warned top officials about the flaw and proposed an updated algorithm that would have flagged the hidden signals. Instead of being heeded, Szarfman was told to cease and desist. Meanwhile, agency officials continued to cite the absence of system alerts as they reassured clinicians and the public about the vaccines’ safety profile.

The consequences of that silence became measurable when the CDC finally ran its PRR analyses in 2022. Walensky publicly stated that the results revealed no additional unexpected safety signals. But when The BMJ examined the underlying analyses, they showed hundreds of adverse events that met the agency’s own alert criteria, including myocarditis, the inflammation of the heart muscle; pericarditis, inflammation of the fluid-filled sac surrounding the heart; Bell’s palsy; and tinnitus. These were precisely the kinds of associations that the FDA’s Bayesian method had failed to trigger, and their appearance in the PRR data suggests that a properly functioning dual-surveillance approach might have surfaced them far earlier.

The investigation also documents that the FDA’s own pharmacovigilance leadership acknowledged the problem internally. In October 2023, the agency’s pharmacovigilance chief wrote in an email to colleagues that the FDA had known of the detection deficiency since the vaccines first rolled out more than two years earlier. The FDA did not respond to The BMJ’s requests for comment on the email or on the broader findings. That admission, coming from within the agency responsible for the flawed method, adds weight to the central claim that the surveillance gap was understood at senior levels and never corrected in public.

The scientists who tried to raise the alarm have now spoken on the record. Szarfman insisted to The BMJ that she had never sought to undermine public confidence in the covid vaccines, expressing her frustration with the observation that very few people understand the statistics, and that this, in her view, was the core of the problem. DuMouchel said he could not explain the officials’ resistance to switching to the updated method, stating simply that he believed they were wrong. He also expressed regret that the FDA had rejected Szarfman’s proposed fixes for VAERS, adding that if the agency had paid attention to her, the system would have performed better.

The investigation reignites a debate that has simmered throughout the pandemic era: what steps were actually taken to safeguard public health from any unintended consequences of the fastest vaccination rollout in history? The documented record now shows an early-warning system whose primary detection tool was structurally incapable of flagging the most relevant signals, a backup method that was postponed for more than a year, internal warnings that were met with a cease-and-desist order, and public reassurances that leaned on the very absence of alerts the flawed system was guaranteed to produce. Whether the myocarditis and other signals eventually identified could have been detected, communicated, and acted upon sooner remains the question that the agencies’ own documents now force into the open.

Subject of Research: Suppressed warnings over a flawed US vaccine adverse event surveillance algorithm during the covid-19 vaccination rollout

Article Title: US officials suppressed warnings over flawed covid vaccine safety algorithm

Article References: US officials suppressed warnings over flawed covid vaccine safety algorithm. (n.d.). Original publication

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Keywords: VAERS, CDC, FDA, mRNA vaccines, myocarditis, vaccine safety surveillance, proportional reporting ratio, empirical Bayesian method, The BMJ investigation, adverse event detection, public health transparency, covid-19 vaccination