Genetics fuel doubt as U.S. tries to keep measles-free

U.S. may – ProPublica’s review of measles viral genomes finds strains circulating in Utah this May closely matched those that sickened people in Texas more than a year earlier—complicating the United States’ effort to keep its measles-free designation. The CDC is running

On a measles map that once looked calm, Utah’s cases suddenly don’t fit the old story. The first confirmed patient in Utah was identified last June. and health officials later determined the person couldn’t have been exposed to measles in another country or even another state. Yet measles kept spreading—through the Utah-Arizona border—and by this May, the virus was still moving.

Now, genetic data is threatening to become the deciding evidence in whether the United States can keep its measles-free distinction.

American children lined up for the world’s first measles shots in the early 1960s. It took nearly 40 years of shoring up immunization programs before a panel of experts declared in 2000 that the United States had eliminated measles within its borders. For a quarter century after that, the U.S. saw outbreaks only when infected travelers brought the virus in from abroad. and those waves didn’t last more than a year.

Those days are gone.

Measles began tearing through the dusty plains of West Texas in January last year. 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.

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 Utah took off that fall and winter and continued into May of this year.

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.

Countries aren’t penalized for losing the status, but officials and public health experts treat it as a blunt measure of whether immunization systems are holding. A loss can signal cracks in a nation’s once rock-solid immunization programs, a loss of faith in vaccines among its people—or both.

To keep the designation, the U.S. will need to make a strong case that measles didn’t spread endemically—moving from person to person in a continuous chain within the country—for more than a year. If. for example. the Texas virus traveled across the Southwest to Utah and kept infecting people there. that would be a problem. But if Utah cases were sparked by a patient who caught measles abroad. that would be a new chain and would restart the clock.

For months. the Centers for Disease Control and Prevention has been 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 state laboratories and the CDC is conducting a more comprehensive investigation.

ProPublica took on the question too. It embarked on its own analysis. reviewing over 1. 800 whole genome sequences. including those released as recently as last month. to compare genetic fingerprints of measles viruses circulating in the U.S. and Canada. The review found 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.

That does not settle the argument by itself. ProPublica’s analysis isn’t a smoking gun that proves endemic spread. because from genetic information alone it’s impossible to tell whether the virus spread from state to state or if it left the country at some point and was brought back by a sick traveler.

Still, the closeness of those viral sequences creates a basic challenge: it will be difficult for the U.S. to prove measles isn’t endemic unless the CDC has additional evidence. Dr. Alberto Severini. a retired molecular virologist and measles expert who spent two decades at Canada’s Public Health Agency. put it bluntly: “unless CDC has something up their sleeves.”.

The genetic picture has wider echoes. The five mutations observed in Texas and Utah were also present in sequences the CDC published of viruses that infected patients last May and June in Iowa, North Dakota, Minnesota and Alaska.

But the genetic trail doesn’t end at U.S. borders. No whole genome sequencing has been made public from cases in either Mexico or the Canadian province of Ontario. where measles has also raged. That matters because whether the virus was spreading continuously in the United States for more than a year—or circulating abroad and then being brought back by travelers—is a key question facing a panel of experts convened by the Pan American Health Organization.

PAHO will decide whether the U.S. keeps its measles-free designation. Canada lost its status last year. PAHO invited the U.S. to make its case in April, but American officials asked for more time to investigate how the virus had been spreading. The review was moved to November.

Daniel Salas, a PAHO official, said thorough analysis like the CDC’s takes time. He said the sequencing effort is trying to find patterns that could eventually say. for example. that a particular mutation of the virus occurred in a different country. in a different place to the current outbreak being analyzed—so that it can be taken into consideration to replace epidemiological information that is missing. “There’s no country that has done this before.”.

For Utah, the missing epidemiological link is the hardest part. Health officials determined the first confirmed patient there. identified last June. couldn’t have been exposed to measles in another country or even another state. Utah State Epidemiologist Dr. Leisha Nolen said her team reviewed where the patient had been and who the patient had been around. but still couldn’t figure out where the virus was caught.

Clues suggested measles had been quietly spreading in the region. A CDC disease detective investigating subsequent cases that spanned the Utah-Arizona border said there had been reports of community members with rashes last June. But the patients declined measles testing and families were often reluctant to answer questions.

Throughout the outbreak, no interviews suggested any patient was exposed in another country, Nolen said, but she and her team cannot rule out the possibility.

ProPublica asked the CDC whether its epidemiologists had linked any of Utah’s measles cases to an international outbreak. The agency wouldn’t say. nor would it directly comment on genetic similarities ProPublica found between viruses in Texas and Utah. In a written statement, a spokesperson said, “Sequencing alone cannot determine whether transmission has been continuous or sustained.”.

While genomic analysis can provide clues. the spokesperson wrote. “These findings must be interpreted alongside epidemiological data. including travel history. exposure information. and known outbreak connections.” The CDC is still working on “a comprehensive analysis of potential linkages among cases and outbreaks” and has gathered additional epidemiological data. but did not elaborate on what that shows.

All of this is happening as the outbreak becomes a political liability for President Donald Trump. Trump picked the founder of an antivaccine organization to be his health secretary. Since Trump’s inauguration last year, there have been more than 4,300 U.S. cases, a high not seen in three decades.

Eliminating endemic measles is the public health equivalent of slaying a dragon—because measles is among the most contagious humans have ever encountered. Patients are infectious even before the telltale rash appears, and the contagion can linger in a room for two hours after they leave.

For years, policymakers built the U.S. immunization system on lessons drawn from measles outbreaks. States aimed for sky-high vaccination rates by making shots mandatory for school and daycare attendance. while the federal government provided them free to low-income kids. When measles still roared back, states such as California and New York cracked down on exemptions to their school mandates. The U.S. helped other countries fight measles as well. not only to prevent deaths but because officials recognized that infectious diseases kept in check abroad are less likely to return to American shores.

During prior U.S. outbreaks, health and political leaders urged Americans to vaccinate their children and reassured the public that the shots were safe.

Trump and HHS Secretary Robert F. Kennedy Jr. have not followed that playbook. Both have fueled doubts about the safety of the MMR shot, which guards against measles, mumps and rubella. Researchers around the world have found the vaccine does not cause autism. Still. at a press conference on autism last fall. Trump said he had heard for years that there was a problem with the combination vaccine and urged parents to insist on separate shots for their kids—even though standalone shots don’t exist in the U.S.

Kennedy has said the vaccine offers protection from measles, but he has repeatedly made the shot sound scarier than the disease. “There are adverse events from the vaccine,” he told Sean Hannity on Fox News last year. “It does cause deaths every year.”

On a podcast, Kennedy said that when he got the virus as a kid, he got to watch television for a week. “I got chicken soup and vitamin A, which nobody can patent,” he said.

Measles kills 1 to 3 out of every 1,000 people infected and can cause deafness, intellectual disability and brain swelling. The Infectious Diseases Society of America said in a “know the facts” post that there have been no deaths shown to be related to the shot in healthy people. “There have been rare cases of deaths from vaccine side effects among children who are immune compromised. which is why it is recommended that they don’t get the vaccine. ” the medical society explained. “That’s why it is so important that everyone who can get vaccinated does so. to protect those who can’t.”.

HHS spokesperson Andrew Nixon said in an email that Kennedy “believes Americans deserve clear information about both the benefits and risks of medical products so they can make informed healthcare decisions in consultation with their healthcare providers.” Nixon said “heavy-handed mandates” contributed to the significant loss of trust in health institutions during the COVID-19 pandemic. “The Secretary maintains that public health agencies rebuild trust through honesty. transparency. and respect for individual choice — not coercion. ” Nixon wrote.

Kennedy has tried to distance himself and the administration from the measles resurgence. He said the U.S. has done a better job of limiting the spread than any other country and pointed to the far higher number of cases in Canada and Mexico, whose populations are much smaller.

White House spokesperson Kush Desai told ProPublica. “Fake News reporters should be spending more time examining why the Trump administration’s efforts to contain America’s measles outbreak has been so much more successful than those of Canada and Mexico instead of regurgitating the same. tired narratives.”.

Kennedy has also reminded lawmakers that the Texas outbreak began before he became health secretary. “We have a global pandemic,” he told senators in April. “It has nothing to do with me.”

Kennedy has been among the most prominent voices in the antivaccine movement for more than a decade.

Dr. Adam Ratner, a pediatric infectious disease physician who wrote a book about measles, said Kennedy has done “everything in his power to undermine confidence in vaccines in the U.S.”

During a measles outbreak in New York City that began in 2018, Ratner treated at least five unvaccinated kids who were hospitalized, including a couple who needed intensive care. Ratner said that not every child escapes the disease with nothing more than memories of screen time and soup.

While most parents still support immunizations. Ratner worries the country no longer has the stomach for policies that once stopped endemic spread. Instead of making school vaccine requirements stricter. some states are working to do away with them altogether in the name of medical freedom. “You need a highly vaccinated population to control the spread,” he said. “In the absence of that. I think that we will have ongoing spread. and we’ll have tragedies like the ones that we saw in West Texas with the two kids who died.”.

The U.S. may find the international travelers it needs to prove the country is still measles free. But experts warn that if the facts remain similar, delay won’t change the underlying trajectory.

“It doesn’t change the fact that there’s been transmission of measles in the United States for over a year,” Severini said. “If people don’t vaccinate, measles is going to be endemic.”

measles MMR vaccine CDC ProPublica Pan American Health Organization PAHO Robert F. Kennedy Jr. Utah outbreak Texas outbreak genomic sequencing Leisha Nolen Alberto Severini