US Scientists Sequence 1,000 Measles Genomes as Outbreaks Surge

CDC data release aims to determine if US has lost its measles elimination status

Apr. 2, 2026 at 1:37pm

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The Centers for Disease Control and Prevention has posted the first batch of 1,000 whole measles virus genomes online, a major effort to analyze whether the US has lost its hard-won measles elimination status due to a surge in outbreaks last year. Scientists say the data release, delayed for months, is a critical step to understand how the disease is spreading across state lines.

Why it matters

Declining vaccination rates, misinformation, and budget cuts have fueled a resurgence of measles, with over 2,200 cases reported in 2025 - the worst year in more than three decades. Whole genome sequencing can reveal if outbreaks are linked by continuous transmission within the US, or separate introductions from abroad, which would mean the country has lost its measles elimination status.

The details

The CDC enlisted the Broad Institute to sequence 1,000 measles virus samples collected from states in 2025 and 2026. The data was slow to be published, with only 8 genomes posted in late March and 154 by April 1st. Researchers say the data should be shared more quickly to understand outbreak patterns. The CDC's measles lab has been understaffed amid layoffs, and the agency is learning how to handle large-scale genome sequencing for the first time.

  • The CDC posted the first batch of 1,000 measles genomes online in late March 2026.
  • The CDC is expected to complete its analysis of the data before April 2026.
  • The Pan American Health Organization was slated to evaluate the US measles status in April 2026, but delayed the review until November to allow the CDC more time.

The players

Centers for Disease Control and Prevention (CDC)

The leading national public health institute in the United States that conducts critical research and provides guidance on disease prevention and control.

Broad Institute

A leading genomics research center that assisted the CDC in sequencing 1,000 measles virus samples.

Kristian Andersen

An evolutionary virologist at the Scripps Research Institute who is following the CDC's measles genome 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 current Secretary of Health and Human Services, 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

“I applaud the science, but the more urgent need is to get measles under control as quickly as possible.”

— Rekha Lakshmanan, Executive Director, The Immunization Partnership

“It definitely shouldn't take the CDC months.”

— Eddie Holmes, Australian Virologist

“The CDC itself is spreading misinformation. I cannot overstate the seriousness of this.”

— Theresa McCarthy Flynn, President, North Carolina Pediatrics Society

What’s next

The CDC is expected to complete its analysis of the 1,000 measles genomes before April 2026, when the Pan American Health Organization was originally scheduled to evaluate the United States' measles elimination status. However, PAHO has delayed the review until November 2026 to allow the CDC more time.

The takeaway

The release of 1,000 measles virus genomes by the CDC is a critical step in determining whether the United States has lost its hard-won measles elimination status, as outbreaks surge across the country. However, political interference, budget cuts, and misinformation have hampered the public health response, underscoring the urgent need to boost vaccination rates and regain control over this preventable disease.