Scientific Integrity Under Fire: How Evidence Was Misrepresented in HHS's COVID Vaccine Policy Reversal

An analysis of cherry-picked studies, flawed citations, and bypassed scientific processes in a controversial health policy decision

Disclaimer: This article reflects the state of knowledge and public health guidance when writing on June 8, 2025. Given the rapidly evolving nature of public health policy and systems, some details, such as the composition of the Advisory Committee on Immunization Practices (ACIP) members, may have changed. The content is intended to illustrate how processes were designed to function at that time and should be interpreted in that context.

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Following an unprecedented announcement by RFK Jr. on X/Twitter last month that COVID-19 vaccines would no longer be recommended for healthy children or pregnant women, Politico reports the Department of Health and Human Services (HHS) distributed an FAQ document to members of Congress outlining “Secretary Kennedy’s justification” for the decision. The document was also circulated to us at Unbiased Science, allowing us the opportunity to review it.

The document claims a commitment to “gold standard science” and describes HHS as “reviewing the science of risk and benefit” behind public health recommendations. It cites evidence that the Secretary says justifies repealing prior recommendations and explains the legal authority under which he claims to act.

The Secretary of HHS holds one of the most powerful roles in shaping U.S. public health policy, and these decisions impact every American. In light of that responsibility, and in the name of science, we carefully reviewed the FAQ’s claims. What we found was deeply troubling.

The actions outlined in the FAQ bypass established health policy and scientific norms. The FAQ misrepresents and falsely cites the evidence, uses outdated data, and risks eroding public trust and the foundation of evidence-based public health.

A Quick Note on Politics, Science, and Health Policy

We know some readers view posts that comment on health policy as “political” or urge us to “stick to the science.” We understand those concerns. At Unbiased Science, we take that responsibility seriously—we genuinely strive to live up to our name.

When developing these posts, we carefully consider all relevant perspectives before sharing them publicly. We’re not perfect, and we always welcome constructive feedback.

It’s also important to acknowledge that health policy involves the application of science, evidence, and values to shape decisions that affect population health. That process inevitably involves “little-p” politics: real-world decisions made in communities that include a range of values and viewpoints.

Our goal is to avoid injecting unnecessary political partisanship into our messages. We aim to hold actions and policies to the same scientific standards, regardless of the political party involved.

In Health Policy, Process Matters

Health policy decisions, such as who should be recommended to receive COVID-19 vaccines, are complex and high-stakes. These decisions can be life-altering for millions of Americans. Because of the stakes, the U.S. has spent decades building systems to guide these decisions with care, transparency, and diverse expertise.

Consider the CDC’s Advisory Committee on Immunization Practices (ACIP). For over 60 years, this independent panel was designed to include voting members from medicine, immunology, public health, nursing, economics, and consumer advocacy. Hundreds more from government agencies, academic institutions, community organizations, and professional societies contribute to the rigorous review process behind the scenes. These systems weren’t created overnight; they have been built and refined over the last 60 years to ensure that vaccine recommendations are rooted in the totality of the scientific evidence.

These systems are imperfect, but they’re designed to prevent what we see now: sweeping decisions made unilaterally, with limited evidence, behind closed doors.

What Happens When You Skip the Process

The HHS announcement discarded the established process. The ACIP was already actively reviewing the evidence and preparing to vote within weeks on which groups should be recommended to receive updated COVID-19 vaccines.

Instead, Secretary Kennedy preempted the process with a blanket decision, then issued a justification that relied on cherry-picked data. Yes, it’s technically true that the CDC Director (or, in this case, the HHS Secretary) can act without ACIP. But that doesn’t make it good science or sound health policy.

The chaos resulting from this decision is already evident. As reported by major news outlets, the CDC's clinical guidance still states that "COVID-19 vaccination is recommended for everyone ages 6 months and older," directly contradicting the HHS announcement. After Kennedy's announcement, the CDC updated its immunization schedule to show COVID-19 vaccines as "recommended vaccination based on shared clinical decision-making" for children rather than removing them entirely, creating further confusion about what the policy means. Even though the new FDA regulatory framework identified pregnancy as a high-risk condition, pregnant individuals are now excluded from vaccine recommendations. Even members of VRBPAC expressed uncertainty about how the new FDA framework would apply to future vaccine development during their recent May 22, 2025, meeting. As for ACIP, we have spoken to people involved, and they are confused too. If the experts are confused, what chance do parents, pregnant people, or clinicians have?

One of the key pillars of trust in health policy is transparency in how decisions are made. That’s why advisory meetings like ACIP (CDC) and VRBPAC (FDA) are publicly broadcast, with evidence in the open and time set aside for public comment before making decisions. In contrast, this decision was made behind closed doors without public input.

The Scientific Claims

The HHS FAQ claims to be based on a scientific review, but it includes just eight references, selectively chosen, which include:

• A preprint that hasn’t been peer reviewed

• Outdated studies

• Authors with a documented history of spreading misinformation

• Misrepresented conclusions of the data

• Studies with flawed methods

• Two citations that don’t even examine the claims the FAQ makes

That’s not a gold-standard review. It’s a weak post-hoc justification dressed up in scientific language. Honestly, with these many egregious errors, we wouldn’t even give it a passing grade in an undergraduate science class.

Let’s Break Down the Claims

The Package Inserts

The FAQ references the Pfizer and Moderna package inserts, which state that safety and efficacy in children under 12 and pregnant individuals have not been established.

That’s technically accurate, but highly misleading. Package inserts are regulatory and legal documents, not comprehensive scientific reviews. They often won’t include the extensive body of real-world evidence, especially studies not conducted by the manufacturer or studies done after the last update. They must also list adverse events reported after vaccination that meet certain legal thresholds, even if the vaccine did not cause them. For years, immunization opponents have taken these documents out of context to sow doubt. Quoting two lines from a package insert is not scientific evidence; it’s a distortion.

Myocarditis and Pericarditis

The FAQ emphasizes the risk of myocarditis and pericarditis (inflammation of the heart and surrounding tissues) following COVID-19 vaccination. Myocarditis was an extremely rare, known side effect observed primarily with the original monovalent COVID-19 vaccine and primary series during the pandemic's first two years, through 2022. However, this risk has virtually disappeared with updated vaccines and schedules since the 2023-2024 season, even in young, healthy men (CDC from April 2025 ACIP meeting [slides #33-40]). The HHS FAQ relies on outdated data and flawed research, exaggerating the risk of vaccine-related myocarditis while failing to acknowledge the significance of COVID-19 infection itself.

Let’s break down the cited studies:

• One article based on VAERS data (up to August 2023) claims that myocarditis reports after COVID-19 vaccination in 2021 were “223 times higher than the average of all vaccines combined for the past 30 years—a 2,500% increase.” But this analysis is methodologically flawed:

  • It uses raw VAERS data, which is a passive, unverified reporting system that cannot establish causality and introduces selection bias.

  • It fails to adjust for:

    • Reporting bias, with no control for reporting propensity changes over time

    • Heightened awareness, with temporal confounding from increased media attention and surveillance

    • The unprecedented scale of the COVID-19 vaccine rollout, which led to denominator issues when compared to a ‘30-year average’ without adjusting for massive differences in vaccination volume and public attention

    • Baseline rates of myocarditis and seasonal variations

  • It exhibits misclassification bias from reports not validated through medical record review or clinical adjudication.

  • The journal has issued an “expression of concern” for the article due to potential issues with the research methodology, conclusions, and author conflicts of interest. An investigation of the article is underway. This expression of concern significantly undermines the credibility of the study’s findings and raises serious questions about why HHS would rely on disputed research to justify major policy changes.

  • Moreover, the study’s senior author, Dr. Peter McCullough, has a documented history of spreading COVID-19 misinformation and had his board certifications revoked. His work includes multiple retracted or disputed studies, which raises major concerns about credibility.

• Another claim references a UK preprint (unpublished and not peer-reviewed) analyzing over 1.7 million children aged 5–15 in 2021-2022. The FAQ misleadingly states that myocarditis and pericarditis occurred only in vaccinated children, implying that these heart conditions are caused exclusively by vaccination and not COVID infection. But:

  • The study’s lead author publicly clarified that this interpretation, which circulated widely on social media, misrepresents the study. Data scientist Colm Andrews from the University of Oxford’s Bennett Institute told fact-checkers that “the study didn’t look specifically at myocarditis and pericarditis following infection” and that the claim in the HHS FAQ is misleading. The research compared vaccinated vs. unvaccinated children, not vaccinated vs. infected, so it does not answer the key question of comparative risk that would inform policy decisions. This question is important because when answered, we see that there was a much higher risk of myocarditis and pericarditis from COVID-19 infection than from the vaccine.

  • The article states that it “reports new medical research that has yet to be evaluated and should not be used to guide clinical practice.”

• Finally, the FAQ cites a Japanese study that used a Japanese database similar to VAERS (up to December 2023). It notes that COVID-19 vaccines were associated with myocarditis, especially in young males under 30. That was true, but it’s only part of the story. This study did not report any new or alarming trends. And like VAERS data, these reports alone aren’t evidence that a vaccine caused an event.

  • This study suffers from the same passive surveillance limitations as VAERS data. It has additional concerns about generalizability - results from Japanese populations may not apply to US populations due to genetic, environmental, and healthcare system differences. Like VAERS data, these association studies cannot establish causation without proper controls.

Critically absent from the HHS FAQ is any mention that COVID-19 infection itself poses a significant risk of myocarditis. Additionally, when post-vaccine myocarditis has been observed, it is generally less severe than post-COVID-19 myocarditis and tends to resolve quickly. This crucial context is completely omitted for an honest risk-benefit analysis.

Bottom line: Scientific evidence demonstrates that the risk of myocarditis after vaccination has virtually disappeared in recent years, particularly with updated vaccines and schedules. In contrast, COVID-19 infection continues to pose a significant risk for myocarditis, even for young males, the demographic previously identified with the highest risk during 2020-2022. A comprehensive risk-benefit analysis consistently shows that vaccination remains the safer choice due to its effectiveness in preventing severe disease and complications, but also because the risk of myocarditis from COVID-19 infection has always outweighed that from vaccination. That’s why the American Academy of Pediatrics, which has issued vaccine guidance for over 90 years, has recommended COVID-19 vaccination for children and will, as always, conduct its own rigorous review to inform future recommendations.

Pregnancy Complications

The FAQ attempts to justify the repeal of a recommendation for pregnant women by citing several studies. However, a closer examination reveals significant discrepancies:

• One claim references this study and states, “a number of studies in pregnant women showed higher rates of fetal loss if vaccination was received before 20 weeks of pregnancy.” Yet this study explicitly concludes the opposite: “SARS-CoV-2 vaccination was not associated with miscarriage.” The lead author of the study, Dr. Maria P. Velez, told Politico, “The results of our manuscript were misinterpreted.” Researchers found “no association between SARS-CoV-2 vaccination and an increased risk of miscarriage.” This raises serious questions about whether the wrong study was cited, the statistical analysis was misunderstood, or the study wasn’t read carefully, if at all.

• Another cited study reported a two percentage point increase in preterm birth for women vaccinated in the second trimester. But the study’s authors note:

• There were no preterm births within two weeks of vaccination,

• Most preterm births were late preterm (less severe),

• And unmeasured confounding (a third factor that makes two things seem connected when they’re not) may have influenced results.

Notably, this tiny increase in late preterm birth for women vaccinated in the second trimester is not supported by the broader scientific literature, which has repeatedly found that COVID-19 vaccination during pregnancy is safe and does not raise the risk of preterm birth (another taste of studies–9,10,11,12). And equally as important, the risk of preterm birth is higher after COVID-19 infection during pregnancy than after vaccination.

• To a degree that raises serious concerns, the FAQ references a study supposedly showing “increased placental blood clotting in pregnant mothers who took the vaccine.” This is entirely inaccurate—the cited study did not evaluate placental clotting, and the statement appears to be either fabricated or incorrect. At the same time, studies have repeatedly found that COVID-19 vaccines do not cause an increase in placental clotting (13,14,15). These same studies also show that COVID-19 infection does cause placental problems, including clotting.

• Inexplicably, the FAQ includes a citation for a study that showed the administration of COVID-19 vaccines was not associated with adverse outcomes after in vitro fertilization. We genuinely have no idea why this study was included in the citations (as it was not referred to in the text), but we appreciate the FAQ author’s acknowledgement of yet another study that contributed to the large body of evidence showing the safety of COVID-19 vaccines in women who are pregnant or trying to conceive.

The totality of evidence regarding COVID-19 vaccination in pregnancy supports that:

• COVID-19 vaccines are safe during pregnancy,

• Infection with COVID-19 is far more dangerous, and

• Vaccination protects both the mother and the baby.

That’s why organizations like the American College of Obstetricians and Gynecologists (ACOG) strongly recommend vaccination during pregnancy. ACOG’s review concludes:

“There is no evidence of adverse maternal or fetal effects from vaccinating pregnant individuals with the COVID-19 vaccine, and a growing body of data demonstrates the safety of such use. None of the COVID-19 vaccines available for use… causes infertility or spontaneous abortion.”

And the risks of COVID-19 infection in pregnancy are real:

• Increased risk of severe illness, ICU admission, and death (9)

• Elevated risk of preterm birth and possible stillbirth (10)

• Greater risk for pregnant individuals with conditions like diabetes, obesity, or heart disease (11)

A Final Note About the Cited References

Correctly citing references is essential for scientific integrity, proper attribution of original work, and transparency about the strength and quality of evidence. However, the FAQ fails even the most basic standards in this case. Beyond the serious concerns we raised about the scientific content and interpretation of the studies, the citations also fall far short of what would be accepted in any peer-reviewed journal or reputable media outlet.

So, we pulled out our favorite citation style guide and looked closer. With only eight references, here are a few of the issues we found:

• One reference listed after footnote “viii” has no corresponding superscript citation in the text, and the DOI leads to an entirely different article than the one cited.

• References “viii” and “ix” do not correspond with claims in the text.

• Reference “ix” includes a duplicated DOI link.

• Reference “vi” omits the name of the journal entirely.

When a document justifying major changes to national health recommendations can’t meet even basic citation standards, it raises serious questions—not just about the conclusions being drawn, but the care, rigor, and integrity behind the process.

A Pattern of Poor Scientific Practice

The HHS FAQ represents more than just flawed policy—it demonstrates a concerning pattern of cherry-picking data, misrepresenting studies, and bypassing established scientific processes. When government agencies abandon rigorous scientific standards in favor of predetermined conclusions, they undermine specific policies and public trust in science itself.

The decision to announce this policy change via social media, bypass expert advisory committees already scheduled to review the evidence, and justify it with a document containing fundamental citation errors and misrepresented studies is unprecedented in modern public health practice.

What Happens Now?

The full implications of these actions remain unclear. While the FAQ insists that children and pregnant women are still "free to consult their healthcare providers regarding COVID-19 vaccination," that statement reflects a fundamental misunderstanding of how access to care works in this country.

What about the 100 million Americans without access to a primary care provider? Will insurance still cover a vaccine that's no longer officially recommended? Will providers and health systems feel comfortable offering—or even stocking—a vaccine that has been politically singled out?

The chaos and confusion already evident, with CDC guidance contradicting HHS announcements and uncertainty about insurance coverage, represent exactly the downstream consequences that independent advisory committees like ACIP were designed to anticipate and address. Until June 9, 2025, when RFK Jr. announced the termination of all ACIP members in a Wall Street Journal op-ed, the committee members were selected based on their scientific expertise, professional achievements, and deep understanding of immunization practices and vaccine-preventable diseases. Their careful deliberations considered the data, infrastructure, access, and equity challenges that define real-world public health.

The ACIP was scheduled to meet on June 25-27th, with COVID-19 vaccines on the agenda. What will replace this 60-year-old institution remains unclear, but given RFK Jr.'s documented history of vaccine opposition, any new appointees are unlikely to reflect the scientific consensus that overwhelmingly supports vaccine safety and efficacy. We are in uncharted territory—not just for COVID vaccines, but for evidence-based vaccine policy itself.

But this isn't just about COVID vaccines. It's about how we make public health decisions.

If science is to remain trustworthy, the process matters. The people making these decisions need to follow the evidence, be transparent about the decision process, and involve the entirety of the experts and systems we've built to guide them.

That didn't happen here.

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So what can you do?

• Keep asking questions.

• Turn to trusted medical organizations (ACOG, AAP, AAFP) and independent experts.

• Support transparency and evidence-based policymaking, no matter who is in charge.

Science is more than just data—it’s a commitment to trust, integrity, and the systems that safeguard our health. In times like these, we don’t need less of that commitment—we need more. The process of transparent review, diverse expertise, and public input isn't bureaucratic red tape. It's how we build recommendations that Americans can trust with their lives.

Stay Curious,

Unbiased Science

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