{"id":35873,"date":"2026-04-02T10:39:28","date_gmt":"2026-04-02T10:39:28","guid":{"rendered":"https:\/\/christiancorner.us\/index.php\/2026\/04\/02\/us-scientists-sequence-1000-genomes-from-measles-a-disease-long-eliminated-by-vaccines\/"},"modified":"2026-04-02T10:39:41","modified_gmt":"2026-04-02T10:39:41","slug":"us-scientists-sequence-1000-genomes-from-measles-a-disease-long-eliminated-by-vaccines","status":"publish","type":"post","link":"https:\/\/christiancorner.us\/index.php\/2026\/04\/02\/us-scientists-sequence-1000-genomes-from-measles-a-disease-long-eliminated-by-vaccines\/","title":{"rendered":"US scientists sequence 1,000 genomes from measles, a disease long eliminated by vaccines"},"content":{"rendered":"\n
\n <\/span><\/p>\n

This week, the Centers for Disease Control and Prevention posted online its first major batch of advanced genetic data from the measles virus that spread last year. Scientists with knowledge of the operation expect the agency to post more in the coming weeks, which will reveal whether the US has lost its hard-won measles elimination status.<\/p>\n

CDC withheld the data for months as a team hard hit by mass layoffs and resignations sifted through the information. But now that the agency’s scientists have posted the first batch of complete measles genomes \u2014 the genetic blueprint of the virus \u2014 the rest “should start to flow more smoothly, at a more rapid pace,” said Christian Anderson, an evolutionary virologist at the Scripps Research Institute who is not involved in the CDC effort but is following it.<\/p>\n

The CDC did not respond to KFF Health News’ queries on its timeline for publishing measles data or analysis. However, once all the data is made public, researchers can run quick preliminary analyzes that will indicate whether the outbreak across the US last year was due to the continued spread of the disease between states rather than isolated introductions from abroad. If persistent transmission continues for a year, it means the US has lost its status as the country that has eliminated measles. That status, which the US has had since 2000, reflects a country’s vaccination rate: two doses of the measles-mumps-rubella vaccine prevents most infections and thus keeps outbreaks from escalating.<\/p>\n

More careful analysis takes several weeks.<\/p>\n

“We should see a report in April,” Anderson said, “assuming there is no political interference.”<\/p>\n

It is the first time the US has applied sophisticated genomic techniques to measles, which disappeared from the country a quarter-century ago due to widespread vaccination.<\/p>\n

Declining vaccination rates, misinformation, and the Trump administration’s budget cuts and slow 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. With 1,575 cases by the end of March this year, it is on track to surpass it.<\/p>\n

Welcoming the science, researchers say that the government’s top priority should be to stop the spread of this virus.<\/p>\n

“I think it’s incredibly important to do whole genome sequencing for outbreaks,” Anderson said, “but we don’t need to do that for measles in the first place, because we have an extremely effective and safe vaccine.”<\/p>\n

“We’re even talking about this, it’s crazy,” he said.<\/p>\n

Health and Human Services Secretary Robert F. Kennedy Jr. and other government officials should sound the alarm about the return of measles and launch a nationwide vaccine campaign, said Rekha Lakshmanan, executive director of The Immunization Partnership, a nonprofit in Houston that advocates for vaccine access.<\/p>\n

“I appreciate the science,” she said, “but the more immediate need is to get measles under control as quickly as possible.”<\/p>\n

Top officials have instead downplayed the seriousness of the disease, and misconceptions about vaccines have been given new life at Kennedy’s CDC. This includes sudden changes to vaccine information on CDC websites Treatment<\/a> The unions say these are not based on evidence and put lives at risk. <\/p>\n

Kennedy continues to promote unproven treatments that may mislead parents into believing they can avoid vaccines without consequences. But joe rogan experience<\/em> In a podcast in late February, Kennedy talked at length about measures to improve America’s health but did not mention vaccines. He said preventive measures could include “holistic medicine, or taking vitamins, or taking vitamin D, which, you know, is kind of miraculous.”<\/p>\n

Neither the Department of Health and Human Services nor the CDC responded to questions from KFF Health News.<\/p>\n

<\/p>\n

1,000 genomes<\/h2>\n

In December, CDC enlisted the help of the Broad Institute in Cambridge, Massachusetts, one of the nation’s leading centers for virus sequencing. Major outbreaks in Texas, Utah, and South Carolina were caused by the same type of measles virus, labeled D8-9171. But since the variant also circulates in Canada and Mexico, researchers need more data to figure out whether it has spread across the states or entered the U.S. multiple times.<\/p>\n

Whole genome sequencing provides that information as viruses evolve over time. The measles virus acquires a mutation every two to four times it is transmitted between people, said Bronwyn MacInnis, director of pathogen surveillance at the Broad.<\/p>\n

“There are enough signals in this data to tease apart the existing questions,” McInnis said, adding, “The main thing is continued transmission within this country.”<\/p>\n

McInnis’ team worked overtime to sequence the entire genome of inactive measles viruses collected from states in 2025 and 2026.<\/p>\n

“We’ve taken about 1,000 samples and sent the genome data back to CDC,” McInnis said. “This is CDC’s data to publish.”<\/p>\n

The CDC did not post any 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 come online.<\/p>\n

“It should be on NCBI within a few weeks of production,” Anderson said, “and it certainly won’t take more than a month when you have an active outbreak.”<\/p>\n

Genomic data provide clues about how outbreaks start and spread. This allows researchers to develop tests, treatments and vaccines \u2013 and detect variants that may evade them.<\/p>\n

Such data was important in the Covid pandemic. Chinese and Australian scientists posted the first SARS-CoV-2 genome online on January 10, 2020, within a week of sequencing. \u201cThis certainly shouldn’t be taking CDC months,\u201d said Australian virologist Eddie Holmes, who helped publish the first coronavirus sequence.<\/p>\n

A CDC scientist told KFF Health News that one reason for the delay is that CDC’s measles laboratory is severely understaffed due to massive layoffs and other upheaval at the agency last year. Another reason, the researcher said, is the learning curve: The CDC and health departments have not had to sequence hundreds of complete measles genomes before now. (KFF Health News agreed not to identify the scientist out of fear of retribution.)<\/p>\n

Unlike the CDC, the Utah Public Health Lab has rapidly shared the measles genome. Most of the approximately 970 measles genomes posted online since Jan. 1, 2025, that were sequenced by state were from Utah, Arizona, South Carolina and other states that were willing to share them.<\/p>\n

“We’ve only got a few samples from Texas that were collected in the middle of their outbreak,” said Kelly Okeson, a genomics researcher with the Utah Department of Health and Human Services. The genomes of the Texas and Utah measles viruses are similar but different, Okson said, meaning intermediate versions of the virus are missing.<\/p>\n

If the genetic code of the virus collected late in the Texas outbreak matched the genetic code of the virus from Utah, it would suggest that the spread was sustained and the country lost its measles-free status. The hundreds of genome sequences still held at CDC probably provide the answer.<\/p>\n

waiting at cdc<\/h2>\n

The CDC hopes to finish its analysis before April, said Daniel Salas, executive manager of the vaccination program at the Pan American Health Organization, which works with the World Health Organization. That’s when PAHO had to evaluate the measles situation in the United States.<\/p>\n

He said PAHO delayed its assessment until the organization’s annual meeting in November, partly because CDC needed more time to conduct the genomic analysis and partly because the measles situations in Mexico, Bolivia and other countries are also under review, and holding separate meetings for each country is inefficient.<\/p>\n

The U.S. is the only country that is using whole genome sequencing to answer the eradication question, Salas said. Typically, countries classify measles viruses according to a small fragment of the gene, then assume that large outbreaks caused by the same variant are linked. Whole genomes provide a more accurate view.<\/p>\n

“If the US can fill in the blanks with genomic data, that’s kind of a success,” Salas said. “This does not mean that other countries will be able to do this kind of analysis,” he said. \u201cIt requires a lot of specialized knowledge and resources.\u201d<\/p>\n

The equipment to sequence and analyze genomes costs more than $100,000, and the cost of processing each sample, including payment to the researchers involved, typically ranges from $100 to $500 per sequence.<\/p>\n

“I’m pro-science, but we shouldn’t be doing this,” said Theresa McCarthy Flynn, president of the North Carolina Pediatrics Society. “We don’t have to have a measles epidemic.”<\/p>\n

Flynn said she regularly fields questions from parents concerned about misinformation spread by Kennedy and anti-vaccine groups, including the group she founded before joining the Trump administration. Parents have also pointed to changes in the CDC’s recommendations and its websites that contradict scientific consensus.<\/p>\n

Before Kennedy took office, a CDC website prominently stated that “vaccines do not cause autism”, and listed several large studies in major scientific journals that refuted the link between vaccines and developmental disorders.<\/p>\n

Last year, the website began saying, “Studies supporting the link have been ignored by health officials.” High-quality studies were replaced by reports 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 CDC’s acting director, Jay Bhattacharya, says vaccines are the best way to prevent measles, he has also weakened vaccine policy. He said the controversial January decision to reduce the number of vaccines recommended for children was based on “gold standard science.” In fact, the new schedule makes America different among peer countries.<\/p>\n

A federal court last month temporarily invalidated the changes in a lawsuit filed by the American Academy of Pediatrics and other groups.<\/p>\n

Bhattacharya has not held briefings with the public or press on the measles surge this year or activated CDC’s emergency capabilities.<\/p>\n

“In general, we have to make a bigger effort to increase vaccination rates in areas where it is lower. We will do a bigger social media push, advertising on vaccinations,” said another CDC scientist, whom KFF Health News agreed not to identify due to fear of retaliation. “The people at CDC want to do this, but the political leadership of the agency has not allowed CDC to do it.”<\/p>\n

Additionally, the Trump administration’s cuts and delays in public health funding have made it harder for local health officials to protect communities. Phillip Huang, director of Dallas County Health and Human Services in Texas, said the department lost more than $4 million when the administration withdrew nearly $11 billion from health departments early last year as measles outbreaks surged in the state.<\/p>\n

“We lost 27 staff members and had to cancel more than 20 of our community vaccination efforts, including those identified in schools with low vaccination rates,” he said. \u201cThere are simultaneous attacks on vaccinations that are making our job difficult.\u201d<\/p>\n<\/p><\/div>\n","protected":false},"excerpt":{"rendered":"

This week, the Centers for Disease Control and Prevention posted online its first major batch of advanced genetic data from the measles virus that spread last year. Scientists with knowledge of the operation expect the agency to post more in the coming weeks, which will reveal whether the US has lost its hard-won measles elimination<\/p>\n","protected":false},"author":1,"featured_media":35874,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[60],"tags":[5069,4078,14679,1324,14680,80,14678,4456],"class_list":["post-35873","post","type-post","status-publish","format-standard","has-post-thumbnail","category-meditation","tag-disease","tag-eliminated","tag-genomes","tag-long","tag-measles","tag-scientists","tag-sequence","tag-vaccines"],"_links":{"self":[{"href":"https:\/\/christiancorner.us\/index.php\/wp-json\/wp\/v2\/posts\/35873","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/christiancorner.us\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/christiancorner.us\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/christiancorner.us\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/christiancorner.us\/index.php\/wp-json\/wp\/v2\/comments?post=35873"}],"version-history":[{"count":1,"href":"https:\/\/christiancorner.us\/index.php\/wp-json\/wp\/v2\/posts\/35873\/revisions"}],"predecessor-version":[{"id":35875,"href":"https:\/\/christiancorner.us\/index.php\/wp-json\/wp\/v2\/posts\/35873\/revisions\/35875"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/christiancorner.us\/index.php\/wp-json\/wp\/v2\/media\/35874"}],"wp:attachment":[{"href":"https:\/\/christiancorner.us\/index.php\/wp-json\/wp\/v2\/media?parent=35873"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/christiancorner.us\/index.php\/wp-json\/wp\/v2\/categories?post=35873"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/christiancorner.us\/index.php\/wp-json\/wp\/v2\/tags?post=35873"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}