Why the FDA tried to bury studies showing vaccines are safe
Jake Scott, MD
A spokesman for the Department of Health and Human Services
(HHS) confirmed the withdrawals on the record, saying the studies were
withdrawn because "the authors drew broad conclusions that were not
supported by the underlying data" and that "the F.D.A. acted to
protect the integrity of its scientific process and ensure that any work
associated with the agency meets its high standards."
The studies are public. Anyone can read them. The FDA's own
scientists, working with the active surveillance system Congress mandated after
the withdrawal of Vioxx, an anti-inflammatory pain reliever, in 2004 after it
was tied to increased heart attacks and strokes, produced findings consistent
with every major post-market analysis of these vaccines published worldwide
since 2023.
The work was buried for reasons that have nothing to do with
the underlying data.
What the studies actually found
One of the COVID vaccine studies, involving US adults 65 and
older, was withdrawn from the
journal Drug Safety after acceptance. It analyzed more
than 7 million Medicare beneficiaries who received the 2023-24 vaccine. The
investigators evaluated 14 specific health outcomes, ranging from heart attacks
and strokes to Guillain-Barré syndrome (GBS), an autoimmune condition that has been
linked to certain vaccines.
They identified one statistically meaningful signal: a small
elevation in anaphylaxis (a severe allergic reaction) following the
Pfizer-BioNTech vaccine. After they adjusted for the possibility that some
"anaphylaxis" billing codes did not represent true cases, the signal
disappeared. The attributable risk, before that adjustment, was less than one
excess case of anaphylaxis per million doses administered. The investigators
concluded that no new safety signals had been identified.
The work was buried for reasons that have nothing to do with the underlying data.
The under-65 2023-24 COVID vaccine study, withdrawn from the
journal Vaccine, examined 4.2 million recipients aged 6
months to 64 years across 17 health outcomes. The investigators flagged a rare
elevation in the risk of febrile seizures (fever-related seizures) on the day
of and the day after Moderna vaccination, in children aged 2 to 5 years.
The exact case count was so small the researchers had to
mask it for patient privacy. Fewer than 11 cases. A separate small signal for
myocarditis (inflammation of the heart muscle) in adolescents lost statistical
significance once the analysis accounted for the seasonal pattern of
myocarditis in the general population. The investigators concluded that no new
safety concerns had been identified.
The Shingrix abstracts blocked from the February conference
were routine updates to safety and effectiveness surveillance the FDA has been
publishing transparently for years. To understand why their suppression
matters, it helps to look at what the agency did with this same vaccine five
years ago.
A precedent: How the agency handled a real signal in 2021
In November 2021, an FDA team led by Ravi Goud, MD, MPH,
with collaborators at the Centers for Medicare & Medicaid Services (CMS)
and the Centers for Disease Control and Prevention (CDC), published an analysis in JAMA
Internal Medicine documenting an increased risk of GBS
following Shingrix, the recombinant herpes zoster vaccine used to prevent
shingles.
The CDC had detected a preliminary statistical signal in its
Vaccine Safety Datalink, comparing GBS rates after Shingrix to GBS rates after
the older shingles vaccine, Zostavax. Rather than dismiss the signal or sit on
it, the agencies launched a full investigation in the Medicare claims database.
The methods were rigorous. The cohort analysis included
roughly 850,000 Shingrix vaccinees and 1.8 million Zostavax vaccinees, all aged
65 or older. A self-controlled case series analysis added events from 2.1
million Shingrix recipients, comparing GBS incidence in the 42 days after each
dose to incidence in days 43 through 183 in the same patients. To rule out
billing artifacts, the team requested actual hospital records and had
independent neurologists adjudicate each case against the standardized Brighton
Collaboration definition.
The surveillance confirmed a real but exceedingly rare
signal. The medical-record-confirmed analysis found a roughly fivefold increase
in GBS risk in the 42 days after vaccination, with an absolute attributable
risk of 5.17 excess GBS cases per million doses. An extended analysis using a
larger pool of cases narrowed the estimate to roughly 3 excess cases per
million doses. The case-series design also let the team isolate when the risk
occurred. It was concentrated almost entirely after the first dose. After the
second dose, the rate ratio dropped to 0.22, with no statistically significant
elevation.
The FDA did not bury this finding. The agency added GBS to
the Shingrix label as a known side effect. Goud and colleagues laid out the
benefit-risk math in plain terms. Using their attributable risk and the trial
efficacy of 97%, they estimated that a fully vaccinated population of 1 million
people would experience about 6.26 excess cases of GBS, while preventing
approximately 7,070 cases of shingles. The authors closed by recommending that
clinicians be aware of the risk and that the benefit-risk balance remained
clearly in favor of vaccination.
The Shingrix abstracts blocked in February were routine
updates to this same surveillance, conducted by the same career scientists,
using the same methodology. According to the Times reporting,
one abstract concerned vaccine effectiveness and found it in line with the
original clinical trial data. The other concerned safety and found an elevated
but low risk of GBS already known to and acted on by the agency. There was no
hidden danger in either abstract, only an updated calculation of numbers the
FDA itself put on the Shingrix label five years ago.
How the methods hold up to standard objections
A persistent claim from critics of mRNA vaccines, including
some who held senior FDA positions during the period of these withdrawals, is
that observational vaccine safety studies suffer from "healthy vaccinee
bias." Vaccinated people, the argument goes, are systematically different
from unvaccinated people, healthier overall, and more likely to seek preventive
care, so comparisons between the two groups can make vaccines look safer than
they truly are.
The argument has merit when applied to studies that compare
vaccinated to unvaccinated populations. It does not apply to the design used in
these studies. A self-controlled case series uses each person as his or her own
control, comparing the rate of an outcome in a defined post-vaccination window
to the rate of the same outcome in a later control window in the same person.
Sex, chronic illness, lifestyle, health-seeking behavior—every personal
characteristic that does not change over the study period—is held constant by
design.
The investigators went further. They adjusted for the
natural seasonal patterns of outcomes like stroke and heart attack, using
month-by-month Medicare incidence from the prior year as a baseline, so that
winter cardiovascular events following fall vaccination would not be
misattributed to the vaccines. They also addressed billing-code noise. A
physician might enter a code for "anaphylaxis" or
"myocarditis" to justify ordering a test that ultimately rules out
the diagnosis, and the code stays in the database. The team used positive
predictive value imputation, which uses prior chart-review data to estimate
what fraction of recorded codes represent true cases, and filtered out the
expected false-positives accordingly.
The anaphylaxis signal in seniors held up after the seasonal
adjustment. It disappeared after the misclassification adjustment. The signal
was a statistical artifact, identified as such by the same rigorous methods
the BEST Initiative was built to
apply.
Blocked COVID studies simply verify prior data
A Nordic cohort study of 23.1
million residents of Denmark, Finland, Norway, and Sweden,
published in JAMA Cardiology in 2022, characterized the
myocarditis risk after the original mRNA COVID vaccines with high precision.
The risk was real, concentrated in young males, and highest after the second
dose, particularly with Moderna.
The investigators wrote that their data were
"compatible with 4 to 7 excess events within 28 days per 100,000 vaccinees
after a second dose of BNT162b2 [Pfizer-BioNTech], and 9 to 28 excess events
within 28 days per 100,000 vaccinees after a second dose of mRNA-1273
[Moderna]." They concluded that the risk needed to be balanced against the
benefits of these vaccines. The paper was not buried. It informed clinical
practice.
In the multinational Global Vaccine Data Network
analysis published in Vaccine in 2024, Faksová
and colleagues pooled data on more than 99 million vaccinated individuals
across study sites in eight countries on four continents. Their analysis
confirmed pre-established safety signals for myocarditis, pericarditis, GBS,
and cerebral venous sinus thrombosis (a rare type of blood clot in the brain).
The pattern was internally consistent across the contributing countries.
In a Danish nationwide cohort of
more than 1.5 million adults aged 65 or older, or otherwise at
high risk, who received the LP.8.1-containing mRNA vaccines used in the 2025-26
season, Hviid et al evaluated 30 prespecified adverse events of special
interest in the 28 days after vaccination. Receipt of the vaccine was not
associated with a statistically significant increased rate of hospital contacts
for any of them.
The suppressed FDA studies are not anomalies. They are
corroborations.
Across the 2023-24, bivalent (two-strain), and JN.1-lineage
COVID vaccine formulations, post-market surveillance has consistently
characterized the same small set of rare, well-defined adverse events.
Myocarditis, concentrated in young males and declining substantially with newer
formulations and longer dosing intervals (in a systematic review my
colleagues and I published in the New England Journal of Medicine in
October, the diagnosis occurred at rates of 1.3 to 3.1 per 100,000 doses in
male adolescents). Anaphylaxis at a few cases per million doses. Rare GBS
signals associated with specific products that have been characterized,
labeled, and managed.
That review synthesized 511 studies across the COVID-19,
RSV, and influenza vaccines and concluded that "ongoing peer-reviewed
evidence supports the safety and effectiveness of immunizations against
Covid-19, RSV, and influenza during the 2025-2026 season."
The suppressed FDA studies are not anomalies. They are
corroborations. The agency's own scientists, looking at the agency's own data,
found exactly what every other major surveillance system in the world has been
finding. The decision to bury their work does not change the underlying
evidence. It changes only the public's access to it.
What the BEST Initiative was built to do
The Biologics Effectiveness and Safety (BEST) Initiative is
the active surveillance arm of the FDA's Center for Biologics Evaluation and
Research (CBER). It exists because passive systems like the Vaccine Adverse
Event Reporting System (VAERS), in which clinicians and patients voluntarily
report events they suspect might be related to a vaccine, generate raw counts
without denominators or control populations and cannot determine
causation.
After the rofecoxib (Vioxx) withdrawal in
2004 made painfully clear how much harm a passive reporting system can miss,
Congress passed the FDA Amendments Act of 2007,
mandating active post-market surveillance covering at least 100 million
Americans. The Sentinel Initiative followed in
2008. BEST, the biologics arm of Sentinel, launched in 2017.
BEST scans electronic health records on tens of millions of
people in near-real time, applying rigorous epidemiologic designs that control
for the biases that skeptics have long argued contaminate observational vaccine
research. The system is built to publish what it finds, whether the finding is
reassuring or whether it identifies a small signal that warrants regulatory
action.
The previously published BEST surveillance studies of COVID
vaccines illustrate what this transparency has looked like in practice. Wong and colleagues openly published four
early-warning statistical signals in elderly Medicare patients
receiving the original mRNA vaccines in 2023. Shoaibi and colleagues followed up later
that year with refined analyses that resolved most of those signals as not
consistently elevated.
Each of these papers had authors in common with the studies
just suppressed. They followed the same methodology. They were published
openly—because that is what the system was built to do.
When the system stops producing public outputs, the loss is
not simply a few papers. It is the credibility of the surveillance enterprise
itself, which is the only thing that allows post-market evidence to function as
a legitimate public good rather than an exercise in agency self-protection.
The other side of the same misleading operation
Last August, HHS Secretary Robert F. Kennedy Jr. terminated
$500 million in BARDA contracts for mRNA vaccine research and pointed to a
181-page bibliography as his scientific justification. I read that document carefully
and wrote about it in STAT shortly afterward.
The lead compiler was a dentist, not an immunologist,
virologist, or vaccine expert. The document originated as a research collection
assembled for a book whose foreword was written by Sen Ron Johnson (R-Wis). It
was not a systematic review. It was a curated reading list, organized around a
conclusion the compilers had already reached.
The substance of the bibliography did not support the
conclusion the secretary drew from it. Most of the cited papers were in vitro
laboratory experiments documenting effects of the SARS-CoV-2 spike protein
produced during natural infection, not during vaccination. Many used
experimental routes of administration with no relevance to human vaccination,
including direct injection into the brain and infusion into cerebrospinal
fluid. Several of the cited papers explicitly concluded that the benefits of
vaccination outweighed the risks of the rare neurologic events they
described.
The Commonwealth Fund estimate that
COVID-19 vaccines prevented approximately 3.2 million American deaths through
2022 was not cited. The Global Vaccine Data Network analysis of 99 million
vaccinated individuals was not cited.
The bibliography manufactured the appearance of an evidence
base for ending mRNA vaccine research. The actual literature, including the
literature the bibliography itself purported to summarize, did not support that
decision.
One half of the operation amplifies the science that fits
a predetermined conclusion. The other half buries the science that does not.
What has happened at the FDA and CDC in the months since is
the other side of the same operation. The Kennedy bibliography elevated
misrepresented evidence to manufacture concern about mRNA vaccines. The FDA
withdrawals and the CDC
suppression last month of the VISION Network's COVID vaccine
effectiveness paper—showing modest protection for 2025-26 vaccines—have
suppressed rigorous evidence that would provide reassurance about those same
vaccines.
One half of the operation amplifies the science that fits a
predetermined conclusion. The other half buries the science that does not. Both
push in the same direction. The public ends up with less reliable information
either way.
What we lose when safety findings don’t reach the public
The career scientists at the FDA and CDC and the contractors
who run BEST built something genuinely remarkable over the past 15 years.
Active surveillance covering tens of millions of Americans. Methods sensitive
enough to detect adverse events occurring at rates of a few per million doses.
Findings made public routinely, including findings of rare risks that warranted
regulatory action and label changes.
The infrastructure exists because Congress decided after
Vioxx that the public deserved it. It works only if the findings reach the
public.
The studies the FDA tried to bury would have told the
American public that the system Congress built is doing its job. The 2023-24
COVID vaccines, evaluated across more than 7 million Medicare beneficiaries and
4.2 million commercial enrollees, showed no new safety signals. The 2025-26
COVID vaccines, evaluated across the CDC's VISION Network of more than 250
emergency departments and urgent care centers and 179 hospitals, reduced
emergency department visits by half and hospitalizations by 55% in immunocompetent
adults.
None of this would have surprised anyone fluent in the
post-market vaccine literature. All of it would have been useful to the
patients and clinicians making real decisions about real vaccines this fall.
The deal Congress struck after Vioxx was straightforward.
The federal government would conduct active surveillance on the vaccines it
licenses and recommends, and tell the public what it finds. When that deal
holds, the system works. When it doesn't, what looks like editorial discretion
from the inside reads from the outside as the cover-up vaccine skeptics have
spent two decades alleging.
The career scientists who actually did the rigorous work do
not get to defend it, because their papers are not out. The vaccinated and the
vaccine-confident lose access to evidence that supports their decisions. The
skeptics get to point at the silence and claim vindication.
The studies suppressed here were not buried because they
showed the vaccines were dangerous. They were buried because they showed the
system was working.
Dr. Scott is a Clinical Associate Professor of
Infectious Diseases at Stanford University School of Medicine and a co-author
of “Updated Evidence for
Covid-19, RSV, and Influenza Vaccines for 2025-2026“ in
the New England Journal of Medicine.
The opinions voiced in CIDRAP Op-Ed pieces are the
authors’ own and do not necessarily represent the official position of CIDRAP.
