US Races to Sequence Measles Genomes as Outbreaks Surge

CDC scrambles to analyze 1,000 samples as measles cases hit 3-decade high

Apr. 5, 2026 at 12:03pm

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The CDC has enlisted the Broad Institute to rapidly sequence the genomes of over 1,000 measles virus samples collected during last year's outbreaks across the US. The data could reveal whether the country has lost its hard-won measles elimination status, but the agency has been slow to publish the findings amid staffing shortages and political interference.

Why it matters

Measles was declared eliminated in the US in 2000 due to high vaccination rates, but declining immunization, misinformation, and the Trump administration's budget cuts have fueled a resurgence. Genomic data is crucial to determine if the outbreaks represent continuous spread within the country or separate introductions from abroad.

The details

The CDC enlisted the Broad Institute in December to sequence the full genomes of over 1,000 measles virus samples collected in 2025-2026. This data can reveal how the virus is evolving and spreading, but the CDC delayed publishing the findings for months. Only 154 genomes were posted online by April 1, far behind the rapid sharing of COVID-19 data early in that pandemic.

  • In December 2025, the CDC enlisted the Broad Institute to sequence 1,000 measles virus genomes.
  • By late March 2026, only 8 of the 1,000 genomes had been posted online.
  • By April 1, 2026, an additional 154 genomes had been published.

The players

Centers for Disease Control and Prevention (CDC)

The US public health agency responsible for monitoring and responding to disease outbreaks, including the recent surge in measles cases.

Broad Institute

A leading genomics research center that was enlisted by the CDC to rapidly sequence over 1,000 measles virus samples.

Kristian Andersen

An evolutionary virologist at the Scripps Research Institute who is following the CDC's measles genomic sequencing efforts.

Bronwyn MacInnis

The director of pathogen surveillance at the Broad Institute, who oversaw the sequencing of 1,000 measles virus samples for the CDC.

Robert F. Kennedy Jr.

The Health and Human Services Secretary who has promoted unproven remedies and spread misinformation about vaccines.

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What they’re saying

“We should see a report in April, assuming no political interference.”

— Kristian Andersen, Evolutionary virologist

“I think it's incredibly important to do whole genome sequencing for outbreaks, but we shouldn't need to do this for measles in the first place, because we have an extremely effective and safe vaccine.”

— Kristian Andersen, Evolutionary virologist

“The risk of measles remains low for most of the United States. CDC has made $8.5 million available to address measles response activities in 7 jurisdictions experiencing outbreaks.”

— Emily Hilliard, HHS spokesperson

What’s next

The CDC is expected to complete its analysis of the measles genome data before April, when the Pan American Health Organization was slated to evaluate the US's measles elimination status. However, PAHO has delayed its evaluation until November to allow more time for the CDC's work.

The takeaway

The CDC's slow release of crucial genomic data on the measles resurgence highlights the agency's struggles with staffing shortages and political interference, even as the US risks losing its hard-won measles elimination status due to declining vaccination rates and misinformation.