Flu and COVID-19 Vaccines: Who Calls the Shots?

“The process of recommending vaccines in the United States has undergone a seismic disruption.”

Helen Y. Chu, MD, MPH et al., “The Path Forward for Vaccine Policy in the United States,” New England Journal of Medicine, July 30, 2025

“What you heard clearly today are the new data published since CDC’s last evidence review does not indicate the emergence of a new safety signal or a sudden drop in effectiveness."

Michael Osterholm, MPH, PhD, director, Center for Infectious Disease Research and Policy, University of Minnesota

A growing list of viral diseases are spreading around the world. In addition, novel viruses could emerge and precipitate the next pandemic. Vaccines are the cornerstone in protection against viruses. Yet, vaccine preparedness in the U.S is in a chaotic state. Nothing could demonstrate this more than the recent controversy over immunization recommendations this fall for the seasonal flu (influenza A virus) and for COVID-19 (SARS-CoV-2 virus). In this week’s Germ Gems post, I focus on the state of the politics, science, and art of vaccination against seasonal flu and COVID-19.

Trust in recommendations from the Centers for Disease Control and Prevention (CDC) eroded.  On February 13, 2025, politics trumped science when Robert F. Kennedy Jr. became Secretary of Health and Human Services (HHS). With Mr. Kennedy in control of the CDC, the stunning track record of the CDC’s world leadership in public health has come to an end. (See, “At Least 600 CDC Employees Are Getting Final Termination Notices, Union Says,” AP News, August 25, 2025, giving an overview of the current chaos at the CDC).  In addition to the myriad of other bad decisions he has made during his short tenure as Secretary of HHS, Mr. Kennedy has completely eroded the public’s trust in the CDC’s recommendations regarding COVID-19 and flu immunizations. 

On May 27, 2025, Mr. Kennedy announced that he had removed the COVID-19 vaccine for healthy children and pregnant women from the CDC’s recommended immunization schedules leaving “clinicians, pharmacist, consumers, and insurers confused about who should get vaccinated against COVID-19 and who should pay for it.” (Rubin, R., “The CDC No Longer Recommends COVID-19 Shots During Pregnancy—Now What?,” JAMA Medical News, July 11. 2025). This serves as a “case study of how Kennedy, founder and former chair of the anti-vaccine organization Children’s Health Defense, is disrupting the US vaccination schedule.”

What’s a physician to do? With the CDC essentially out of the picture, physicians will now have to turn to their professional sources for advice about vaccinations. These are trusted professional organizations dedicated to recommending vaccines that are proven safe and effective. For pediatricians (those specializing in children’s health), it is the American Academy of Pediatrics (AAP). For internists (those focusing on adults), it is the American College of Physicians. And for family medicine physicians (those caring for all ages), it is the American Academy of Family Physicians.  Additionally, programs like the non-profit “Vaccine Integrity Project,” supported by the University of Minnesota’s Center for Infectious Disease Research and Policy, provide deeply researched expert advice regarding vaccines for all professional organizations.

Updates on influenza vaccination. Now is the time to consider getting your flu shot. The flu season generally lasts from October through May. Therefore, the optimal time for getting your shot is during September and October thereby protecting you before the flu season ramps up and ensuring that your immunity doesn’t fade before the flu season ends. (It usually takes about two weeks after vaccination for your body to build up enough protective antibodies.)

The AAP recommends that all healthy people 6 months and older be vaccinated against influenza for the 2025-2026 season. The vaccine has shown good efficacy in pregnant and nonpregnant women and in older adults. In the AAP’s view, the controversial issue of the vaccine additive Thimerosal is of little or no concern since it’s known to be safe and was already removed from all childhood vaccines in 2001.

New means of flu prevention are also on the horizon. They include a new flu vaccine as well as a new and highly effective drug. Moderna, one of the key developers of mRNA vaccines, recently announced promising efficacy results from a large mRNA flu vaccine trial. But on August 4, 2025, Secretary Kennedy cancelled $500 million in mRNA research funding. What effect RFK Jr.’s mandate to discontinue research on mRNA vaccines will have not only on this vaccine but also on this line of mRNA vaccine research is unknown but very worrisome.

Then there is the one-shot flu drug CD388 (zanamivir). This drug outperformed flu vaccines in recent clinical trials. Some experts consider the results of CD388 trails as one of the most exciting advances for influenza prevention. (Cohen, J.,“One-shot flu drug may beat vaccines,” Science Adviser, July 3, 2025). Yet, the fate of CD388 is also unclear. (As it is a flu drug, not a flu vaccine, perhaps Mr. Kennedy will let the research go forward.)

Updates on COVID-19 vaccines. A recent study reported in JAMA Health Forum suggested that COVID-19 vaccinations prevented an estimated 2.5 million deaths worldwide between 2020 and 2024 and saved nearly 15 million life-years.  But, COVID-19 infections are on the rise again. On August 19, 2025, the CDC reported that COVID-19 infections were increasing in 36 states. So do you need a COVID-19 vaccination (booster)?

Following the advice of infectious disease experts, the CDC initially recommended annual COVID-19 boosters for all Americans 6 months and older. Then on May 20, 2025, Vinay Prasad, director of the Center for Biologics Evaluation and Research, and the Federal Drug Administration (FDA) Commissioner, Martin Makary, announced new changes on how FDA would evaluate COVID-19 vaccines. (Prasad, V., Makary, M., “An Evidence-Based Approach to COVID-19 vaccination,” New England Journal of Medicine, May 20, 2025). They took issue with the recommendation for COVID-19 boosters for everyone 6 months and older claiming a low COVID-19-related mortality of young children. Subsequently, Mr. Kennedy announced that the CDC was no longer recommending the COVID-19 vaccine for healthy children or pregnant women. No new evidence was cited to support his decision.

On August 19, 2025, for the first time in 30 years, the APA issued its own vaccine recommendations—recommendations that substantially diverged from those of the CDC. The APA strongly recommended COVID-19 shots for children ages 6 months to 2 years. The AAP pointed out that 57% of pediatric hospitalizations occur in children less that 2 years of age and that a majority (89%) of children and adolescents hospitalized for COVID-19 had not received a dose of the most recently recommended vaccine.

The APA’s recommendation flew in the face of the CDC’s recommendation not to vaccinate young children and fueled the flames of controversy about COVID-19 vaccination. It was also the genesis for Mr. Kennedy’s bogus claim that “recommendations that diverge from the CDC’s official list are not shielded from liability under the 1986 Vaccine Injury Act.” (See, Frieden, J., “RFK Jr. Warns Docs of Liability if They Stray From CDC on Vaccines,” MedPage Today, August 22, 2025).

Decisions about vaccinations—who’s in charge? Suffice it to say, the damage RFK Jr. has done to our trust in the CDC is catastrophic. (See, e.g., “RFK Jr and MAHA: dangerous, emboldened, and escalating,” The Lancet, August 23, 2025). And his thinly vailed threats to physicians who waver from the CDC’s recommendations on vaccines is totally outrageous.

While the COVID-19 vaccine formula for 2025-2026 for use in the U.S. beginning in the fall 2025 has been known for some time, this vaccine booster is not yet available at American pharmacies. Nonetheless, if you are an older adult, I strongly recommend getting the COVID-19 booster when it becomes available.

That being said, recommendations on immunizations for the flu and COVID-19 are merely recommendations. Ultimately, you are in charge of all decisions about these immunizations for yourself, or if you’re a parent, decisions about vaccinating your children. But make an informed decision.  Get advice from a trusted health care professional be it a family practitioner, a pediatrician or an internist. (Sadly, 20-30% of American adults lack a primary care doctor and physician assistants fulfill this role in many settings.) The flu and COVID-19 vaccines are safe and effective; they save lives. And the life they save could be yours or your child’s.