This week, the Centers for Diseases 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. <\/p>\n
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 \u2014 the genetic blueprint of the viruses \u2014 the rest should \u201cstart flowing more smoothly at a more rapid cadence,\u201d said Kristian Andersen, an evolutionary virologist at the Scripps Research Institute who isn\u2019t involved with the CDC\u2019s effort but is following it.<\/p>\n
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\u2019s vaccination rates: Two doses of the measles-mumps-rubella vaccine prevent most infections and so stop outbreaks from growing.<\/p>\n
More careful analyses take weeks.<\/p>\n
\u201cWe should see a report in April,\u201d Andersen said, \u201cassuming no political interference.\u201d<\/p>\n
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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.<\/p>\n
Declining vaccination rates, misinformation, and the Trump administration\u2019s 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.<\/p>\n
While welcoming the science, researchers say the government\u2019s top priority should be to stop the virus from spreading.<\/p>\n
\u201cI think it\u2019s incredibly important to do whole genome sequencing for outbreaks,\u201d Andersen said, \u201cbut we shouldn\u2019t need to do this for measles in the first place, because we have an extremely effective and safe vaccine.\u201d<\/p>\n
\u201cThat we\u2019re even talking about this is nuts,\u201d he added.<\/p>\n
Health and Human Services Secretary Robert F. Kennedy Jr. and other government officials should sound an alarm about measles\u2019 comeback and launch nationwide vaccine campaigns, said Rekha Lakshmanan, executive director of The Immunization Partnership, a nonprofit in Houston that advocates for vaccine access. <\/p>\n
\u201cI applaud the science,\u201d she said, \u201cbut the more urgent need is to get measles under control as quickly as possible.\u201d<\/p>\n Top officials have instead downplayed the seriousness of the disease, and false notions about vaccines have been granted new life in Kennedy\u2019s CDC. This includes abrupt changes to vaccine information on CDC websites that medical associations say aren\u2019t based on evidence and endanger lives.\u00a0<\/p>\n Kennedy continues to promote unproven remedies that could mislead parents into believing that they can avoid vaccines without consequence. On the Joe Rogan Experience<\/em> podcast in late February, Kennedy spoke at length about measures to improve America\u2019s health but didn\u2019t mention vaccines. He said preventive measures could entail \u201cholistic medicine, or take vitamins, or take vitamin D, which is, as you know, it\u2019s kind of miraculous.\u201d<\/p>\n Neither the Department of Health and Human Services nor the CDC responded to queries from KFF Health News.<\/p>\n 1,000 Genomes<\/strong><\/p>\n In December, the CDC enlisted the help of one of the country\u2019s 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.<\/p>\n 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.<\/p>\n \u201cThere is enough signal in this data to tease apart questions at hand,\u201d MacInnis said, \u201cthe main one being sustained transmission within this country.\u201d<\/p>\n MacInnis\u2019 team worked overtime to sequence the entire genomes of inactivated measles viruses that had been collected from states in 2025 and 2026.<\/p>\n \u201cWe\u2019ve done about 1,000 samples and delivered the genome data back to the CDC,\u201d sending it on a rolling basis since December, MacInnis said. \u201cThis is the CDC\u2019s data to publish.\u201d<\/p>\n The CDC didn\u2019t 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.<\/p>\n \u201cIt should be on NCBI within a couple of weeks of being produced,\u201d Andersen said, \u201cand certainly not take longer than a month when you have an active outbreak.\u201d<\/p>\n Genomic data holds clues about how outbreaks start and spread. It allows researchers to develop tests, treatments, and vaccines \u2014 and detect variants that might evade them.<\/p>\n 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. \u201cIt definitely shouldn\u2019t take the CDC months,\u201d said Eddie Holmes, the Australian virologist who helped publish the first coronavirus sequence.<\/p>\n One reason for the delay is that the CDC\u2019s 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\u2019t needed to sequence hundreds of whole measles genomes before now. (KFF Health News agreed not to identify the scientist, who feared retaliation.)<\/p>\n 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.<\/p>\n \u201cWe\u2019ve only got a handful of samples from Texas that were collected kind of in the middle of their outbreak,\u201d 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.<\/p>\n If the genetic code of viruses collected late in the Texas outbreak are a closer match to those from Utah\u2019s, 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.<\/p>\n Waiting on the CDC<\/strong><\/p>\n 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\u2019s when PAHO was slated to evaluate the United States\u2019 measles status.<\/p>\n He said PAHO delayed its evaluation until the organization\u2019s 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.<\/p>\n 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.<\/p>\n \u201cIf the U.S. can fill in the blanks with genomic data, that\u2019s a sort of breakthrough,\u201d Salas said. \u201cThat doesn\u2019t mean other countries are going to be able to pull off this kind of analysis,\u201d he added. \u201cIt takes a lot of specialized knowledge and resources.\u201d<\/p>\n 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.<\/p>\n \u201cI\u2019m pro-science, but we shouldn\u2019t have to do this,\u201d said Theresa McCarthy Flynn, president of the North Carolina Pediatrics Society. \u201cWe don\u2019t have to have a measles epidemic.\u201d <\/p>\n 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\u2019s recommendations and to its websites that are at odds with the scientific consensus.<\/p>\n Before Kennedy took the helm, a CDC website said \u201cVaccines do not cause autism\u201d in prominent type, and listed several large studies in premier scientific journals that refuted a link between vaccines and developmental disorders.<\/p>\n Last year, the website shifted to saying, \u201cStudies supporting a link have been ignored by health authorities.\u201d The high-quality studies were replaced with a report from a single investigator who has ties to anti-vaccine groups.<\/p>\n \u201cThe CDC itself is spreading misinformation,\u201d Flynn said. \u201cI cannot overstate the seriousness of this.\u201d<\/p>\n 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 \u201cgold standard science.\u201d In fact, the new schedule makes the U.S. an outlier among peer nations.<\/p>\n A federal court temporarily invalidated the change last month in a lawsuit brought by the American Academy of Pediatrics and other groups.<\/p>\n Bhattacharya hasn\u2019t held briefings with the public or the press on the surge of measles this year or activated the CDC\u2019s emergency capabilities.<\/p>\n \u201cNormally, we\u2019d have a big push to get vaccination rates up in areas where it\u2019s low. We\u2019d do a big social media push, put out ads on getting vaccinated,\u201d said another CDC scientist whom KFF Health News agreed not to identify, because of fears of retaliation. \u201cPeople at the CDC want to do this, but political leadership at the agency has not allowed the CDC to do it.\u201d<\/p>\n Further, the Trump administration\u2019s 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.<\/p>\n \u201cWe lost 27 staff and had to cancel over 20 of our community vaccination efforts, including to schools identified as having low vaccination rates,\u201d he said. \u201cThere are simultaneous attacks on immunizations that are making our jobs harder.\u201d<\/p>\n![\"An](\"https:\/\/kffhealthnews.org\/wp-content\/uploads\/sites\/2\/2026\/04\/Broad_05.jpg\")
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