The American Academy of Pediatrics has urged parents to get their youngest children vaccinated for Covid, part of a broader effort by medical organisations to bypass Health and Human Services Secretary Robert F. Kennedy jnr and his criticism of broadly administering coronavirus vaccines.

Kennedy blasted the medical association in response and described it as beholden to corporate interests.

The AAP is recommending that all children aged from 6 months to 23 months receive a coronavirus vaccine to help protect against serious illness. Children in that age group are especially vulnerable to becoming hospitalised for Covid, the AAP said in its vaccine guidance for parents and paediatricians before the fall-winter respiratory season.

The medical association’s guidance contradicts what Kennedy declared in May when he posted a video on X saying healthy children should no longer receive the vaccine, arguing there is no clinical data to justify repeatedly giving them coronavirus shots. Under Kennedy, the vaccine recommendation process has been upended, resulting in widespread confusion among paediatricians, public health officials and medical associations.

“The majority of what we’ve seen from the secretary has been a pretty clearly orchestrated strategy to sow distrust in vaccines,” said Sean O’Leary, a physician who heads the AAP’s infectious-diseases committee. “We make our recommendations based on what’s in the best interest of the health of children.”

In an X post, Kennedy responded to the AAP’s new vaccine recommendations by calling them “corporate-friendly” and blasting the medical organisation for receiving donations from vaccine manufacturers.

He said the organisation should disclose its “corporate entanglements” and conflicts of interest “so that Americans may ask whether the AAP’s recommendations reflect public health interest, or are, perhaps, just a pay-to-play scheme to promote commercial ambitions of AAP’s Big Pharma benefactors”.

Susan Kressly, AAP’s president, said her group welcomes an opportunity to meet Kennedy to discuss the recommendations.

“This attack on the integrity of paediatricians is unfortunate, but it does not change the facts,” Kressly said in a statement. “We are transparent about our funders​, follow rigorous conflict-of-interest disclosures and maintain safeguards to ensure the integrity and independence of our guidance.”

The country is in the midst of a summer uptick in coronavirus cases, and the future of vaccine access is uncertain.

The Centres for Disease Control and Prevention (CDC) did not go as far as Kennedy directed and did not remove coronavirus vaccines from the childhood immunisation schedule. Instead, the public health agency softened its recommendation for all children to receive an annual coronavirus shot. It now recommends parents consult a doctor to decide whether to vaccinate their children.

The AAP took a similar approach for older children. Its new guide says healthy children ages 2 to 18 can receive a coronavirus vaccine if their parents or guardians want them to have that protection.

Few parents do. The CDC estimates that 13% of all eligible children are up to date on coronavirus vaccines, as well as 4.5% of children between the ages of 6 months and 23 months.

By issuing a broader coronavirus vaccine recommendation for young children, the AAP is trying to boost uptake and keep the shots free. Between October 2022 and April 2024, a little more than half of children between the ages of 6 months and 23 months admitted to intensive care for Covid had no underlying conditions, a CDC study found.

Still, the vast majority of children infected by coronavirus will have mild symptoms, and few will become hospitalised. Health officials say it has become difficult to measure the effectiveness of coronavirus vaccines in young children because the vaccination rates are so low.

Limited data shows the 2024-2025 coronavirus vaccines provided extra protection against severe illness in children and adults compared with people who did not receive a vaccine, according to CDC data presented in June.

But paediatric infectious-disease specialists have argued that regularly vaccinating children makes sense as a public health strategy because evidence has shown each year that protection in children is similar to that seen in adults.

Federal officials have yet to approve or recommend an updated coronavirus vaccine, which usually debuts in late summer. The Food and Drug Administration (FDA) has signalled it would not license upcoming coronavirus vaccines for otherwise healthy children.

Kennedy recently fired all members of the CDC’s Advisory Committee on Immunisation Practices, a group of experts who decide who should receive FDA-approved or authorised vaccines. Four of the seven members Kennedy appointed as replacements have been publicly critical of the broad use of coronavirus vaccines.

For the past three decades, the AAP and the CDC have been mostly aligned in their vaccine recommendations – until now.

The AAP’s schedule “differs from recent recommendations of the Advisory Committee on Immunisation Practices (Acip) of the CDC, which was overhauled this year and replaced with individuals who have a history of spreading vaccine misinformation”, the organisation said in a statement.

Retsef Levi, an Acip member who has denounced the use of mRNA coronavirus vaccines, criticised the AAP’s recommendation in an X post, arguing Covid poses “zero risk” to babies and the shots could damage their hearts. His message was reposted by Robert Malone, another Acip member who has been critical of coronavirus vaccines.

Under federal law, insurers must cover the cost of Acip-recommended vaccinations. The AAP and other professional organisations have been holding discussions with insurance companies to continue covering the shots based on guidance from professional associations rather than the federal Government.

O’Leary said insurers “are signalling that they are committed to covering our recommendations”. Ahip (formerly America’s Health Insurance Plans), the major insurance lobby, has said its members are committed to continuing to pay for respiratory virus vaccines this season.

The new Acip panel did not make any coronavirus recommendations when it met for the first time in late June.

It may not even convene a special meeting to discuss the coronavirus vaccines until mid-September, according to industry employees and CDC officials who spoke on the condition of anonymity to share sensitive information. That timing has become more uncertain after the August 8 shooting at the CDC that severely damaged several buildings and traumatised CDC staff. The Acip is scheduled to hold a meeting in October.

The AAP’s full vaccine guidance, published on Tuesday in the organisation’s clinical guidebook for infectious-diseases prevention and treatment, represents formal recommendations for immunisations for infants, children and adolescents against 18 diseases. Its recommendations for flu and respiratory syncytial virus, or RSV, are essentially the same as what federal health officials, including Kennedy, have recommended.