What ProPublica Found in the Genetic Code of America’s Measles Outbreaks — ProPublica

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American children lined up for the world’s first measles shots in the early 1960s, but it took nearly 40 years of shoring up immunization programs before the infamous contagion had been so thoroughly controlled that a panel of experts declared in 2000 that the United States had eliminated measles within its borders.<br>For a quarter century, the U.S. only saw outbreaks when infected travelers brought the virus in from abroad. The resulting waves of measles didn’t last more than a year.<br>Those days are gone.<br>Measles began tearing through the dusty plains of West Texas in January last year, and since then, all but a handful of states have seen cases. Two unvaccinated Texas girls and an adult across the border in New Mexico died before the West Texas outbreak seemed to burn out last July.<br>By then, measles was popping up in Utah, and state health officials couldn’t tell where the earliest patients had caught the virus. Infections in that state took off that fall and winter and continued into May of this year.<br>The Texas and Utah cases now sit at the center of an unusually technical — and politically fraught — question: whether the United States will lose its measles-free distinction.<br>Countries aren’t penalized for losing the status, but it’s an indication of cracks in a nation’s once rock-solid immunization programs, a loss of faith in vaccines among its people — or both.<br>To have any chance of keeping the designation, the U.S. will need to make a strong case that measles didn’t spread endemically — from person to person in a continuous chain within the country for more than a year. If the Texas virus, for example, made its way across the Southwest to Utah and continued infecting people there, that would be a problem. But if cases in Utah were instead sparked by a patient who caught measles abroad, that would be a new chain, restarting the clock.<br>For clues, the Centers for Disease Control and Prevention is analyzing the full genetic code of measles viruses that infected patients. Last November, the CDC’s leader at the time said preliminary genomic analysis suggested the Utah cases were not directly linked to those in Texas. A spokesperson for the Department of Health and Human Services told ProPublica that the work was done by the state laboratories and the CDC is conducting a more comprehensive investigation.<br>ProPublica embarked on its own analysis, reviewing over 1,800 whole genome sequences, including those released as recently as last month, to compare the genetic fingerprints of measles viruses circulating in the U.S. and Canada. This showed that the measles virus still spreading in Utah as of this May is very closely related to the one that sickened Texans over a year ago.<br>ProPublica’s analysis isn’t a smoking gun that proves endemic spread. It’s impossible to tell from this information whether the virus spread from state to state or if it at some point left the country and was brought back by a sick traveler.<br>But given how similar the viruses are in the sequences ProPublica identified, it’s going to be difficult for the U.S. to prove measles isn’t endemic — “unless CDC has something up their sleeves,” said Dr. Alberto Severini, a retired molecular virologist and measles expert who spent two decades at Canada’s Public Health Agency.<br>This is a small portion of the genetic code from a sample of measles virus collected in Utah in May 2026. Each letter represents one of the four molecules that encode the unique instructions for how the virus is built and operates.

ProPublica compared it to the sequence from a virus collected during the first days of the Texas outbreak in January 2025.

The two sequences are nearly identical. But when you look closely, mutations — tiny changes in the virus’s genetic code — begin to appear. These mutations form a distinct fingerprint.

Out of the nearly 16,000 genetic letters in each sequence, only 12 differ between the original Texas virus and the Utah virus...