COVID-19 Update: Confusion and Chaos on Vaccine Recommendations

“The COVID-19 pandemic dramatically changed the fabric of science and health care, and its effects and the lessons learned will reverberate for decades to come.”

James M. Goldman, MD, Darilyn Meyer, MD “Flying the Plane While Building It: Lessons From the COVID-19 Pandemic”

“My career in public health and vaccinology started with a deep-seated desire to help the most vulnerable members of our population, and that is not something I’m able to continue doing in this role.”

Dr. Lakshmi Panagiotakopoulos (June 4, 2025 email to the CDC Advisory Committee on Immunizations Practice upon resignation)

The COVID-19 pandemic is now into its sixth year, and SARS-CoV-2, the novel coronavirus that caused the pandemic, has thus far killed close to 8 million people. No one can predict with certainty when—or if— this rampage will end. The uncertainty is rooted both in the “nature of the beast,” that is the intrinsic impossibly of predicting when pandemics will emerge as well as end, and also in human nature—in this case, the politicalization of COVID-19 in the U.S. (See “Experts Blast HHS Leaders for Defying Norms, Sidelining CDC,” MedPage Today, May 30, 2025). Fortunately, there is a cadre of devoted public health experts who continue to collect and analyze data and provide insights on what’s new with the virus and how best to stop it, that is, what vaccines work. My goal in writing this week’s Germ Gems post is to update readers on information on the current COVID-19 vaccine recommendations.

Origin of COVID-19. One of the most important and contentious controversies in the scientific circles of those studying SARS-CoV-2 is where did it come from (originate). Did the virus spillover in nature—most likely from a bat, with the raccoon dog as a reservoir animal host—or was it “leaked,” that is inadvertently carried from the Wuhan Institute of Virology to the Wuhan Seafood Market?

The lab leak hypothesis suggests that Chinese scientists, helped by U.S. experts and fueled with federal dollars, created SARS-CoV-2 in a the Wuhan Institute of Virology in so-called “gain of function” experiments.  There’s been a spate of recent publications favoring the “Lab Leak Hypothesis,” all of which I find unconvincing. (See, e.g.,  “SARS-CoV-2 Origin: Lab Leak Hypothesis Gains Momentum,” Medscape, May 12, 2025).

Nonetheless, right now, it is politically incorrect to disavow this hypothesis. Just last week, FBI Director Kash Patel announced a “breakthrough” amid the ongoing COVID-19 origin investigations—the recovery of Dr. Anthony Fauci’s phones and devices used early in the pandemic which might show the suppression of information on the origins of SARS-CoV-2 and support a lab leak conspiracy.

It remains to be seen what pertinent information, if any, might be contained on Dr. Fauci’s devices. The fact is that we may never know where SARS-CoV-2 originated. But for me, and for now, the spillover hypothesis remains the most tenable explanation. (See, “Origin of COVID-19: Did It Start with a Spillover in Stall A?, ” Germ Gems, October 2, 2024).

What SARS-CoV-2 variant is the current trouble maker? Since December 2019, the original SARS-CoV-2, known as the L strain, has mutated countless times giving rise to a dizzying number of variants and subvariants. Thankfully, the technology is available to track these variants and to describe new culprits. This information is crucial for determining the strain that vaccines should target.

In May 2025, the U.S. Food and Drug Administration (FDA) announced newer strains of the JN.1 variant should be the 2025-2026 vaccine target, specifically the LP.1 strain, which has been surging in Asia. (On June 7, 2025 a new variant known as NB.1.81 was identified, but so far no glaring differences between the symptoms of NB.1.8.1 and other variants of SARS-CoV-2 have been seen.) The new COVID-19 vaccines (2025-2026) should be available this fall. (But given all the chaos, don’t hold your breath.)

Who should get vaccinated and why? Many people are confused about who should receive the new COVID-19 vaccine and, more importantly, why they need to be vaccinated. (See, “COVID vaccine changes confuse and upset some parents and families,” Health Watch, June 3, 2025). This sad state of affairs isn’t surprising as not only is the Centers for Disease Control and Prevention (CDC), the entity that sets the immunization schedules for both adults and children, in disarray but the Advisory Committee for Immunization Practices (ACIP) has also been gutted. On June 9, 2025, Health and Human Services Secretary Robert F. Kennedy Jr. announced that he was “retiring” all 17 members of the ACIP and made the bald-faced assertion that the ACIP had “become little more than a rubber stamp for any vaccine.”  (For those readers outside the medical field, the members of the ACIP are independent medical and public health experts who advise and vote on the CDC’s vaccine recommendations.)

The answer to why you should get the vaccine is simple: the COVID-19 vaccines work. While not 100% effective at preventing COVID-19, the vaccines have been shown to save lives and prevent hospitalizations. According to a study conducted by the World Health Organization (WHO), between December 2020 and March 2023, over 1.4 million lives were saved in the WHO European Region alone due to COVID-19 vaccination efforts. For just 7 months in 2023-2024 in the U.S., CDC investigators estimate that COVID vaccinations averted more than 5,000 in-hospital deaths, 13,000 intensive care admissions, and 68,000 hospitalizations.  

The answer to who should get vaccinated is more complicated. The CDC recommends, and all health experts agree, that older adults and people who are immunocompromised are candidates for the new vaccine. But, in a short video posted on X in late May, Secretary Kennedy, on a whim, announced that under his watch the CDC would no longer advise pregnant women and healthy children to get vaccinated against COVID-19. Hence, there remains confusion as to whether pregnant women and healthy children should be vaccinated.

Where the guidelines are unclear, the CDC currently recommends “Shared Decision-Making,” that is discuss the situation with your doctor and then make a decision. In my opinion, this recommendation says nothing; it is waffling.

All decisions about vaccination should be discussed with your healthcare provider even childhood vaccines that are mandated for various reasons to protect the health of the child as well as the public. Nonetheless, I agree with my infectious diseases colleagues that pregnant women who are in an “immunocompromised” state due to hormones that prevent fetal loss should be advised to get the COVID-19 vaccine. (See, “Infectious Disease Docs Slam New COVID Vaccine Recommendations,” MedPage Today, June 6, 2025).

Why is there so much confusions about the COVID-19 vaccines? The answer is Robert F. Kennedy, Jr.—one of the world’s leading anti-vaxxers but nonetheless the U.S. Secretary of Health and Human Services. A rapidly growing number of articles question his capabilities. (See, e.g., “How to Think About COVID-19 Vaccines in the Era of Kennedy,” New Yorker, May 31, 2025; “Rewriting of Covid vaccine recommendations has doctors and other experts worried,” STAT, June 5, 2025; “Despite Kennedy’s claims, vaccines have been tested in placebo-controlled studies—nearly 260 of them.” CNN, June 6, 2025; “Calls for RFK Jr. to Resign Grow Lounder,” MedPage Today, June 5, 2025). To put it bluntly, this “secretary” has no clothes; he is not qualified to lead the CDC, FDA, and National Institutes of Health.

The enemy in the COVID-19 pandemic is submicroscopic; it is the novel coronavirus SARS-CoV-2. It should be crystal clear to everybody that we need the best and brightest scientists, public health experts, and doctors to lead the war against SARS-CoV-2. And vaccines—which in my view are are the single biggest achievement of modern medicine—are our major weapon.