Katelyn Messer is among the researchers at the Broad Institute in Cambridge, Massachusetts, who have sequenced 1,000 whole genomes of measles viruses that spread in the U.S. between Jan. 20, 2025, and Jan. 20, 2026. The data will help reveal whether the country has lost its measles elimination status. (Amy Maxmen/KFF Health News)
This week, the Centers for Disease Control and Prevention posted online its first large tranche of advanced genetic data from measles viruses spreading last year. Scientists with knowledge of the operation expect the agency to post heaps more in weeks to come, revealing whether the U.S. has lost its hard-won measles elimination status.
The CDC withheld the data for months as a team hit hard by mass layoffs and resignations sorted through the information. But now that scientists at the agency have posted their first batch of whole measles genomes — the genetic blueprint of the viruses — the rest should “start flowing more smoothly at a more rapid cadence,” said Kristian Andersen, an evolutionary virologist at the Scripps Research Institute who isn’t involved with the CDC’s effort but is following it.
The CDC did not answer queries from KFF Health News on its timeline for publishing measles data or analyses. However, once all the data is public, researchers can run quick initial analyses that will signal whether outbreaks across the U.S. last year resulted from the continuous spread of the disease between states, rather than separate introductions from abroad. If there was continuous transmission for a year, that means the U.S. has lost its status as a country that has eliminated measles. That status, which the U.S. has held since 2000, reflects a country’s vaccination rates: Two doses of the measles-mumps-rubella vaccine prevent most infections and so stop outbreaks from growing.
More careful analyses take weeks.
“We should see a report in April,” Andersen said, “assuming no political interference.”
This is the first time that the U.S. has applied sophisticated genomic techniques to measles, which largely disappeared from the country a quarter-century ago because of broad vaccine uptake.
Declining vaccination rates, misinformation, and the Trump administration’s budget cuts and lagging response to outbreaks have fueled a resurgence of the disease. With at least 2,285 cases in 44 states, 2025 was the worst year for measles in more than three decades. This year is on track to surpass that, with 1,575 cases as of late March.
While welcoming the science, researchers say the government’s top priority should be to stop the virus from spreading.
“I think it’s incredibly important to do whole genome sequencing for outbreaks,” Andersen said, “but we shouldn’t need to do this for measles in the first place, because we have an extremely effective and safe vaccine.”
“That we’re even talking about this is nuts,” he added.
Health and Human Services Secretary Robert F. Kennedy Jr. and other government officials should sound an alarm about measles’ comeback and launch nationwide vaccine campaigns, said Rekha Lakshmanan, executive director of The Immunization Partnership, a nonprofit in Houston that advocates for vaccine access.
“I applaud the science,” she said, “but the more urgent need is to get measles under control as quickly as possible.”
Top officials have instead downplayed the seriousness of the disease, and false notions about vaccines have been granted new life in Kennedy’s CDC. This includes abrupt changes to vaccine information on CDC websites that medical associations say aren’t based on evidence and endanger lives.
Kennedy continues to promote unproven remedies that could mislead parents into believing that they can avoid vaccines without consequence. On the Joe Rogan Experience podcast in late February, Kennedy spoke at length about measures to improve America’s health but didn’t mention vaccines. He said preventive measures could entail “holistic medicine, or take vitamins, or take vitamin D, which is, as you know, it’s kind of miraculous.”
“The risk of measles remains low for most of the United States,” HHS spokesperson Emily Hilliard wrote. “CDC has made $8.5 million available to address measles response activities in 7 jurisdictions experiencing outbreaks,” she wrote. “The CDC, HHS principles, and the Secretary have been vocal that the MMR vaccine is the best way to protect yourself against measles.”
1,000 Genomes
In December, the CDC enlisted the help of one of the country’s leading centers for virus sequencing, the Broad Institute in Cambridge, Massachusetts. Major outbreaks in Texas, Utah, and South Carolina had been fueled by the same type of measles virus, labeled D8-9171. But since that type also circulates in Canada and Mexico, researchers need more data to discern whether it spread among states or entered the U.S. multiple times.
Whole genome sequencing provides that information because viruses evolve over time. The measles virus acquires a mutation every two to four transmissions between people, said Bronwyn MacInnis, director of pathogen surveillance at the Broad.
“There is enough signal in this data to tease apart questions at hand,” MacInnis said, “the main one being sustained transmission within this country.”
MacInnis’ team worked overtime to sequence the entire genomes of inactivated measles viruses that had been collected from states in 2025 and 2026.
“We’ve done about 1,000 samples and delivered the genome data back to the CDC,” sending it on a rolling basis since December, MacInnis said. “This is the CDC’s data to publish.”
The CDC didn’t post a single one of those genomes until late March, when eight appeared on a public database hosted by the National Center for Biotechnology Information. By April 1, an additional 154 had gone online.
“It should be on NCBI within a couple of weeks of being produced,” Andersen said, “and certainly not take longer than a month when you have an active outbreak.”
Genomic data holds clues about how outbreaks start and spread. It allows researchers to develop tests, treatments, and vaccines — and detect variants that might evade them.
Such data was critical in the covid pandemic. Chinese and Australian scientists posted the first SARS-CoV-2 genome online on Jan. 10, 2020, within a week of sequencing it. “It definitely shouldn’t take the CDC months,” said Eddie Holmes, the Australian virologist who helped publish the first coronavirus sequence.
One reason for the delay is that the CDC’s measles lab has been sorely understaffed amid mass layoffs and other turmoil at the agency over the past year, a CDC scientist told KFF Health News. Another reason, the researcher added, is a learning curve: The CDC and health departments haven’t needed to sequence hundreds of whole measles genomes before now. (KFF Health News agreed not to identify the scientist, who feared retaliation.)
In contrast with the CDC, the Utah Public Health Lab has shared measles genomes rapidly. Most of some 970 measles genomes posted online since Jan. 1, 2025, were sequenced by the state, hailing from Utah, Arizona, South Carolina, and other states willing to share them.
“We’ve only got a handful of samples from Texas that were collected kind of in the middle of their outbreak,” said Kelly Oakeson, a genomics researcher at the Utah Department of Health and Human Services. The genomes of the Texas and Utah measles viruses are similar but distinct, Oakeson said, meaning that intermediate versions of the virus are missing.
If the genetic code of viruses collected late in the Texas outbreak are a closer match to those from Utah’s, that will suggest that spread was continuous and the country has lost its measles-free status. The hundreds of genome sequences still sitting at the CDC probably hold the answer.
Waiting on the CDC
The CDC expected to finish its analysis before April, said Daniel Salas, executive manager of the immunization program at the Pan American Health Organization, which works with the World Health Organization. That’s when PAHO was slated to evaluate the United States’ measles status.
He said PAHO delayed its evaluation until the organization’s annual meeting in November, partly because the CDC needed more time to do the genomic analysis and partly because the measles status of Mexico, Bolivia, and other countries is also under review, and holding staggered meetings for each country is inefficient.
The U.S. is the only country using whole genome sequencing to answer the elimination question, Salas said. Typically, countries classify measles viruses according to a tiny snippet of genes, then assume that large outbreaks caused by the same type are linked. Whole genomes provide a more accurate view.
“If the U.S. can fill in the blanks with genomic data, that’s a sort of breakthrough,” Salas said. “That doesn’t mean other countries are going to be able to pull off this kind of analysis,” he added. “It takes a lot of specialized knowledge and resources.”
Equipment to sequence and analyze genomes costs upward of $100,000, and the cost to process each sample, including paying the researchers involved, typically ranges from $100 to $500 per sequence.
“I’m pro-science, but we shouldn’t have to do this,” said Theresa McCarthy Flynn, president of the North Carolina Pediatrics Society. “We don’t have to have a measles epidemic.”
Flynn said she regularly fields questions from parents concerned by misinformation spread by Kennedy and anti-vaccine groups, including the one he founded before joining the Trump administration. Parents have also pointed to changes in the CDC’s recommendations and to its websites that are at odds with the scientific consensus.
Before Kennedy took the helm, a CDC website said “Vaccines do not cause autism” in prominent type, and listed several large studies in premier scientific journals that refuted a link between vaccines and developmental disorders.
Last year, the website shifted to saying, “Studies supporting a link have been ignored by health authorities.” The high-quality studies were replaced with a report from a single investigator who has ties to anti-vaccine groups. In an email to KFF Health News, HHS spokesperson Hilliard echoed the altered website’s claims about vaccines, disregarding extensive studies on the topic.
Flynn, of the pediatrics association, said, “The CDC itself is spreading misinformation about vaccines. I cannot overstate the seriousness of this.”
Although the acting director of the CDC, Jay Bhattacharya, says vaccines are the best way to prevent measles, he too has undermined vaccine policy. He said the controversial January decision to reduce the number of vaccines recommended to children was based on “gold standard science.” In fact, the new schedule makes the U.S. an outlier among peer nations. Hilliard wrote that the updated schedule was “aligning U.S. guidance with international norms.”
A federal court temporarily invalidated the change last month in a lawsuit brought by the American Academy of Pediatrics and other groups.
Bhattacharya hasn’t held briefings with the public or the press on the surge of measles this year or activated the CDC’s emergency capabilities.
“Normally, we’d have a big push to get vaccination rates up in areas where it’s low. We’d do a big social media push, put out ads on getting vaccinated,” said another CDC scientist whom KFF Health News agreed not to identify, because of fears of retaliation. “People at the CDC want to do this, but political leadership at the agency has not allowed the CDC to do it.”
Further, the Trump administration’s cuts and delays to public health funds have made it hard for local health officials to protect communities. Philip Huang, director at Dallas County Health and Human Services in Texas, said the department lost over $4 million when the administration clawed back about $11 billion from health departments early last year as a measles outbreak surged in the state.
“We lost 27 staff and had to cancel over 20 of our community vaccination efforts, including to schools identified as having low vaccination rates,” he said. “There are simultaneous attacks on immunizations that are making our jobs harder.”
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This article first appeared on KFF Health News and is republished here under a Creative Commons Attribution-NoDerivatives 4.0 International License.
