Measles Genome Sequencing Race Intensifies to Confirm or Refute Ongoing Transmission

Public health teams are racing to sequence measles virus genomes to determine whether the United States has lost its measles elimination status held since 2000, with the CDC posting 162 genomes by April 2025 after months of delays caused by understaffing from mass layoffs. The U.S. recorded 2,285 measles cases across 44 states in 2025—the worst year in three decades—and 1,575 cases by late March 2026, with major outbreaks in Texas, Utah, and South Carolina linked to the same D8-9171 virus strain. The sequencing effort, supported by the Broad Institute processing about 1,000 samples and Utah's public health lab sequencing most of 970 genomes, aims to detect mutation patterns that reveal whether transmission has been continuous for a year, which would cost the U.S. its elimination status. The crisis has intensified amid declining vaccination rates, Trump administration budget cuts including $11 billion clawed back from health departments, and controversial CDC messaging changes under HHS Secretary Robert F. Kennedy Jr. that a federal court temporarily blocked.

CDC's Delayed Release of Measles Genome Sequencing Data

• ▪The Broad Institute worked overtime to sequence the entire genomes of inactivated measles viruses collected from states in 2025 and 2026
• ▪The Centers for Disease Control and Prevention did not post a single measles genome until late March 2025, when eight appeared on a public database hosted by the National Center for Biotechnology Information
• ▪The Broad Institute sequenced about 1,000 measles samples and delivered the genome data back to the Centers for Disease Control and Prevention on a rolling basis since December 2024
• ▪The Centers for Disease Control and Prevention posted online its first large tranche of advanced genetic data from measles viruses spreading in 2024
• ▪By April 1, 2025, an additional 154 measles genomes had been posted online by the Centers for Disease Control and Prevention
• ▪The Utah Public Health Lab sequenced most of some 970 measles genomes posted online since January 1, 2025

Implications for U.S. Measles Elimination Status

• ▪The United States had 1,575 measles cases as of late March 2026
• ▪Major measles outbreaks in Texas, Utah, and South Carolina had been fueled by the same type of measles virus, labeled D8-9171
• ▪The United States has held measles elimination status since 2000
• ▪The United States had at least 2,285 measles cases in 44 states in 2025, the worst year for measles in more than three decades
• ▪Equipment to sequence and analyze genomes costs upward of $100,000
• ▪The Pan American Health Organization delayed its evaluation of the United States' measles elimination status until the organization's annual meeting in November 2026

Trump Administration's Response and Vaccine Misinformation

• ▪The Centers for Disease Control and Prevention made $8.5 million available to address measles response activities in 7 jurisdictions experiencing outbreaks

Impact of Budget Cuts and Staffing on Public Health Response

• ▪The Centers for Disease Control and Prevention enlisted the help of the Broad Institute in Cambridge, Massachusetts in December 2024
• ▪The Trump administration clawed back about $11 billion from health departments early in 2025 as a measles outbreak surged in Texas
• ▪Dallas County Health and Human Services in Texas lost over $4 million when the Trump administration clawed back about $11 billion from health departments early in 2025

Perspective of Local health departments

• ▪Dallas County Health and Human Services in Texas lost over $4 million in federal funding during an active measles outbreak