The Vaccine Intelligence Report: September 30-October 6

The Vaccine Intelligence Report

September 30–October 6, 2026

The Vaccine Intelligence Report—brought to you by Vaccinate Your Family—provides clear, fact-based updates on vaccine policy, research, and public health each week. This report is part of Viral Truths, a resource designed to cut through the noise, offering concise information to help navigate the evolving immunization landscape.

THIS WEEK AT A GLANCE:

  • A coalition of 17 states renewed its legal challenge to federal vaccine policy changes, filing an amended complaint targeting the revised childhood immunization schedule, Kennedy’s ACIP appointments, and the end of the universal hepatitis B birth dose recommendation
  • More than 2,500 physicians urged the Senate to reject FDA Commissioner nominee Dr. Heidi Overton, citing concerns about her role in recent vaccine policy changes and the agency’s scientific independence
  • Kennedy announced a new NIH initiative focused on researching and treating vaccine injuries, though few details have yet been made public
  • Florida will hold a public hearing on a proposed rule to make hepatitis B, chickenpox, Hib, and pneumococcal vaccines optional for school and daycare attendance
  • The West Virginia Supreme Court agreed to hear oral arguments over whether the state must allow religious or philosophical exemptions from school immunization requirements
  • The U.S. has reported more than 4,000 measles cases this year; Pennsylvania has surpassed 1,000 cases and reported a fifth measles-associated death, and New York has declared a statewide emergency amid rising cases
  • Flu activity is increasing unusually early in the season, with infections growing or likely growing in 48 states even as national activity remains low
  • The federal Vaccines.gov locator remains nonfunctional as fall vaccination efforts ramp up, creating an additional access barrier for people seeking flu, Covid, and RSV vaccines

NEED TO KNOW

States Renew Legal Challenge to Federal Vaccine Policy Changes

  • A coalition of 17 states has filed an amended lawsuit challenging changes to the federal childhood immunization schedule and Health and Human Services (HHS) Secretary Robert F. Kennedy Jr.’s overhaul of the Advisory Committee on Immunization Practices (ACIP).
    • The states first sued HHS in February, arguing that the Administration unlawfully changed the childhood immunization schedule and replaced all 17 voting members of ACIP without following required procedures.
    • The January schedule removed six vaccines—including Covid, influenza (flu), and hepatitis B—from the category universally recommended for children, among other changes. Due to an injunction in the American Academy of Pediatrics (AAP) and co-plaintiffs’ related lawsuit against HHS, the schedule has since reverted to the July 2025 schedule while litigation proceeds.
  • In September, U.S. District Judge Vince Chhabria dismissed the states’ claims related to ACIP, finding that they had not adequately shown that the committee’s reconstitution caused them direct harm. However, he allowed the states to amend their complaint and try again.
  • The amended complaint, filed October 2, seeks to address those concerns by detailing how the federal changes have forced states to revise laws, insurance rules, Medicaid policies, and immunization guidance—or risk disruptions to vaccine access and public health programs.
    • New York and Vermont have also joined the lawsuit brought by the Attorneys General of Arizona, California, Colorado, Connecticut, Delaware, Maine, Maryland, Michigan, Minnesota, New Jersey, New Mexico, Oregon, Rhode Island, and Wisconsin, as well as the governor of Pennsylvania.
  • The states are asking the court to invalidate the revised childhood schedule, Kennedy’s ACIP appointments, and the committee’s decision to end the universal hepatitis B birth dose recommendation. They argue that the actions violated the Administrative Procedure Act because they were undertaken without adequate scientific review or required procedures.
  • The amended complaint gives the states another opportunity to challenge the Administration’s broader vaccine policy changes, though the court has already expressed skepticism about whether they can establish standing on the ACIP claims.
  • Separately, the Administration’s appeal of the preliminary injunction in the AAP lawsuit is also moving forward. The U.S. Court of Appeals for the First Circuit heard oral arguments on Tuesday (Oct. 6) on the ruling that blocked the revised childhood immunization schedule, Kennedy’s ACIP appointments, and votes taken by the reconstituted committee.

Physician Coalition Urges Senate to Reject Overton Nomination

  • More than 2,500 physicians across all 50 states, Washington, D.C., and Puerto Rico signed a September 30 letter urging the Senate to reject Dr. Heidi Overton’s nomination to lead the Food and Drug Administration (FDA), citing concerns about her record on vaccine policy and the agency’s scientific independence.
  • The letter, organized by the Committee to Protect Health Care, focused in part on Overton’s role in the Administration’s recent childhood vaccine policy changes.
    • The physicians pointed to her support for the August Executive Order calling for the combined measles, mumps, and rubella (MMR) vaccine to be offered as separate measles, mumps, and rubella shots, arguing that the change would add cost and complexity while undermining confidence in a vaccine with a longstanding safety and effectiveness record.
    • The group argued that the FDA Commissioner must be willing to follow evidence even when it conflicts with political preferences and listen to career scientists, physicians, patients, and researchers when making regulatory decisions.
  • Overton’s nomination remains before the Senate Health, Education, Labor, and Pensions (HELP) Committee following her September 24 confirmation hearing. A committee vote is not expected until after the midterm elections, and Republicans’ narrow margin on the panel heightens uncertainty surrounding her confirmation.

NIH Launches New Vaccine Injury Research Initiative

  • On Monday (Oct. 5), Kennedy announced a new National Institutes of Health (NIH) initiative focused on researching and treating people who report vaccine-related injuries.
    • Kennedy—along with NIH Director Dr. Jay Bhattacharya, Centers for Disease Control and Prevention (CDC) Director Dr. Erica Schwartz, and Acting FDA Commissioner Kyle Diamantas—attended a ribbon-cutting for a new NIH clinic that will study and care for patients with suspected vaccine injuries.
    • The broader effort also includes plans to modernize vaccine safety monitoring and a proposal to reimburse healthcare providers for time spent evaluating and reporting suspected adverse events.
  • The initiative represents another expansion of the Administration’s focus on vaccine injury, following recent efforts to broaden how suspected injuries are identified, tracked, and potentially compensated.
    • Serious vaccine injuries can occur but are rare, and a health problem occurring after vaccination does not necessarily mean the vaccine caused it. Federal programs already monitor vaccine safety and provide compensation in cases where qualifying vaccine-related injuries are established.
  • Additional details—including the NIH initiative’s research priorities, funding, study design, and how suspected injuries will be evaluated—have not yet been publicly released.

STATE POLICY

Florida Moves Forward with Hearing to Consider Removing Four School Immunization Requirements

  • The Florida Department of Health will hold a public hearing Thursday (Oct. 8) on a proposed rule to remove school and daycare immunization requirements for hepatitis B, chickenpox (varicella), Haemophilus influenzaetype b (Hib), and pneumococcal disease and instead make the vaccines optional.
    • Because requirements for these four vaccines were added through agency rules, the department can remove them without legislative approval. The proposed rule does not affect other immunization requirements, including MMR and polio, which can only be modified through legislative action.
  • The proposal is part of Florida Surgeon General Dr. Joseph Ladapo’s broader push to roll back immunization requirements.
    • It also comes amid growing concern about vaccine-preventable diseases, including recent deaths associated with measles (five people in Pennsylvania) and Hib (one child in Montana).
  • The Florida AAP chapter opposes the changes, warning they could further reduce vaccination rates and increase the risk of vaccine-preventable disease.

 West Virginia Supreme Court Will Hear Arguments in School Immunization Exemption Case

  • The West Virginia Supreme Court has agreed to hear oral arguments in the ongoing dispute over whether the state must allow religious or philosophical exemptions to school immunization requirements.
    • The case stems from a lower court ruling that blocked schools from enforcing the requirements against families seeking such exemptions; that ruling remains on hold during the appeal.
  • The dispute follows Governor Patrick Morrisey’s 2025 Executive Order establishing a religious exemption process, despite lawmakers rejecting legislation that would have established exemptions in state law. The Supreme Court has not yet announced a date for oral arguments.
  • The case could have major implications for West Virginia’s school immunization policy, ultimately determining whether the state can continue allowing only medical exemptions or must recognize broader religious exemptions under the Equal Protection for Religion Act.

OUTBREAK OUTLOOK

Measles: 4,020 cases have been reported nationally in 2026, including an increase of 464 cases over the past two weeks (Oct. 2).

  • Pennsylvania confirmed a new measles death last week (Sep. 30), bringing the state’s total to five measles-associated deaths this year. In 2025, the U.S. recorded three measles-associated deaths.
    • The state’s outbreak has reached 1,004 total cases in 2026, including 106 new confirmed cases in the last seven days (Oct. 5).
  • New York, which neighbors Pennsylvania, declared a statewide disaster emergency (Oct. 5) over the ongoing measles outbreak, which has reached 108 cases as of October 3.
    • The declaration gives health officials broader authority to respond to the outbreak, including by expanding which healthcare providers are able to administer vaccines.
  • New research from Johns Hopkins University found that a single measles case during an outbreak incurs medical and public health response costs averaging $43,203.65.
  • For more on other states driving recent measles activity, see here.

Covid: Infections are growing or likely growing in 19 states (Sep. 30). National Covid activity is low (Oct. 2), with overall acute respiratory illness remaining very low.

Flu: Infections are growing or likely growing in 48 states (Sep. 30). Nationally, seasonal flu activity is low but increasing (Oct. 2) headed into respiratory virus season.

Federal Vaccine Locator Remains Offline as Respiratory Virus Season Begins

  • The federal Vaccines.gov search tool remains nonfunctional as flu, Covid, and respiratory syncytial virus (RSV) vaccination efforts ramp up for the fall respiratory virus season.
  • The CDC-run website is intended to help people locate pharmacies and other providers offering vaccines. A notice on the site says its functionality “may be impacted while it is being updated,” but HHS has not provided a timeline for when the search tool will be restored.
    • It is unclear exactly how long the locator has been unavailable. Similar problems were reported as far back as December 2025, suggesting the issue may predate the current respiratory season.
  • The outage creates an additional access barrier at a time when people are being encouraged to seek seasonal vaccines. Individuals can instead use this Vaccine Locator tool to find nearby pharmacies, health centers, and local health departments for more information or to schedule an appointment.

WHAT TO WATCH

ACIP Meeting Remains Scheduled Amid Ongoing Legal Uncertainty

  • ACIP is currently scheduled to meet October 21–23, which would mark the committee’s first meeting since December 2025. The CDC continues to list the three-day meeting on its 2026 calendar.
    • ACIP’s previously scheduled March and June meetings were canceled due to ongoing litigation over Kennedy’s overhaul of the committee and subsequent changes to federal vaccine policy.
  • Whether the October meeting will proceed—and who would participate—remains uncertain as those legal challenges continue. The committee’s membership and actions taken since its 2025 reconstitution remain central issues in the related lawsuits.
  • As of October 7, the CDC has not posted an agenda or other meeting materials for the scheduled meeting.ACIP generally meets three times each year to review scientific evidence and develop federal vaccine recommendations, making the October meeting particularly significant after two consecutive cancellations.
    • Federal advisory committee meetings generally must be announced in the Federal Register at least seven calendar days in advance and include a summary of the agenda or topics to be discussed.
    • If the meeting moves forward, the agenda would provide the first indication of which vaccine recommendations the committee may revisit or consider after nearly a year without meeting.

CDC Seeks Comment on Public Health Emergency Response Funding Process

  • The CDC published (Oct. 5) a proposed information collection related to its Public Health Crisis Response (PHCR) Cooperative Agreement, which is designed to help the agency rapidly distribute funding to eligible jurisdictions and organizations during major public health emergencies.
  • The cooperative agreement would maintain a list of approved but unfunded applicants that could receive federal support when emergency funding becomes available. Funding could support initial response activities as well as countermeasures and mitigation, surge management, and bio-surveillance.
  • The CDC is seeking three years of approval to collect application information for the program. Public comments are due December 4.

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