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An invisible killer
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A flesh-eating fungus is expanding its range in the American West – and scientists suspect climate change is driving the spread
Erik McIntyre, 53, became paralyzed after contracting Valley fever, which is caused by the fungus coccidioides.
BAKERSFIELD, Calif.
At some point, Erik McIntyre inhaled the fungal spores. He couldn’t see them, or feel them, and it was weeks before he began to lose energy, to drop weight, to cough up blood at a karaoke bar in Arizona.
Now that he’s paralyzed from Valley fever, in a nursing home at age 53, the former U.S. Navy electrician’s day begins at 5 a.m. with a rectal tube procedure to release gas trapped in his stomach. The antifungal injections that left him retching and shaking are less frequent now, and the lesions where the fungus grew on his face and arms have faded to scars. But he knows he will never be cured, or probably walk again.
“I try not to dwell on what could have been,” he said.
McIntyre can imagine the moment he encountered those microscopic spores. He remembers driving across dusty Phoenix suburbs with his windows down. But he can’t be sure.
These days, the fungus could be anywhere.
Valley fever has long haunted the American Southwest: Soldiers on dusty military bases, prisoners in wind-swept jails, construction workers pushing new suburbs farther into deserts have all encountered coccidioides, the flesh-eating fungus that causes Valley fever. But the threat is growing. Cases have roughly quadrupled over the past two decades, according to the Centers for Disease Control and Prevention.
A key reason for Valley fever’s spread, researchers say, may be human-driven climate change — and they warn that a much larger area of the United States will become vulnerable to the disease in the decades to come. The fungus thrives in dry soils, rides on plumes of dust and booms after periods of extreme drought — the exact cycles that scientists say have grown more intense and widespread across the American West due to the warming climate.
While science is not yet able to show a definitive link between the rising case counts and higher temperatures, the connection seems clear to many of the front-line health workers grappling with the disease.
“I cannot think of any other infection that is so closely entwined with climate change,” said Rasha Kuran, an infectious-disease specialist at the University of California at Los Angeles who is one of McIntyre’s doctors.
Today, Valley fever affects tens of thousands — probably hundreds of thousands, federal officials say — of people each year, and in rare cases, such as McIntyre’s, it can be extremely debilitating, even fatal. The illness costs about $1.5 billion per year just in the two most prevalent states, Arizona and California. “Cocci,” as researchers call the fungus, is primarily found in the Southwest but also in parts of Central and South America.
The Human Limit
In the United States, it kills a few hundred people each year, according to federal officials — about as many as West Nile virus, the leading cause of mosquito-borne disease in the continental United States. Valley fever has sickened archaeologists sifting Native American artifacts in Utah and New York high school students on a service trip building houses near Tijuana, Mexico.
Public health officials warn that the illness could become more prevalent as drought pushes more agricultural fields into fallow ground, subdivisions sprout in the desert, and the West dries out. About a decade ago, the fungus turned up among the arid hills of Eastern Washington state, rewriting the map of where it was known to be endemic. Cases in California appear to be marching north from their traditional home in the San Joaquin Valley, where the illness got its name.
Morgan Gorris, a staff scientist at Los Alamos National Laboratory, projected that as the climate warms, the fungus could spread across much of the western half of the country by the end of the century.
“What was once a disease that was primarily limited to the Southwestern United States would become a disease of the Western United States,” Gorris said.
While some scientists suspect the fungus’s widening reach is connected to climate change, the connection is so new that they are trying to ascertain basic facts about where it lives and how it might be spreading. Even in places where cocci is prevalent, it can be patchy and maddening to find. Climate change could be fueling the fungus’s transmission in several ways: moving with migrating rodents, more frequent dust storms or expanding wildfires — or emerging from places it has long been hiding as conditions get drier.
“We have to figure out where it’s at — and where it’s going,” Paul Keim, a professor of microbiology at Northern Arizona University, told a conference of Valley fever researchers earlier this month.
These mysteries have pushed a small but ardent band of scientists on a wide-ranging fungal hunt across the West. With drones and air filters, dirt samples and data on dogs’ blood — animals also get Valley fever — they are determined to untangle cocci’s knot.
In California, where more than 1,000 people are hospitalized with Valley fever each year, this search is particularly urgent. Cocci has been shown to flourish after abnormally wet winters like the one the state just experienced. And researchers are bracing for an explosion of cases as the ground dries, said Jennifer Head, a University of Michigan epidemiologist who studies the fungus.
This fall, she predicted, “is when we’ll start to see a huge spike in Valley fever.”
The cocci hunt
In a barren expanse of Southern California scrubland, Head crouched down and fed a long-handled spoon into a rat hole.
Wearing an N95 mask and blue plastic gloves, she filled several test tubes with dry, crumbling soil from the Carrizo Plain National Monument. Then she turned to her colleague and asked for a bit more protection.
“I feel like I could use an ethanol spritz,” Head said, holding out her hands.
Head and her colleagues were scouring this sun-blasted patch of the southern San Joaquin Valley in September in an effort to pinpoint where cocci lives and unravel how it might be spreading.
Out here among the saltbush and vinegar weed is an endless web of rodent burrows — home to squirrels, mice and the giant kangaroo rat, an endangered species the size of a baked potato. When University of California at Berkeley scientists began coming here to study these rodents in 2007, it didn’t take long before they started getting sick.
“A really serious fatigue and a lack of appetite. For a month,” said Tim Bean, then a UC Berkeley ecologist who came down with Valley fever a couple of years into his research on the Carrizo Plain. “It sucked.”
But it turned out to be a perfect place to hunt for fungus.
There has been a known link between rodents and cocci since the early 1940s. More recently, UC Berkeley mycologist John Taylor and colleagues discovered that cocci had lost genes that other fungi use to eat plants and gained those for devouring meat.
“These fungi evolved to eat animals,” he said. And a favorite meal: dead rats.
Taylor believes cocci lives not so much in the soil as in the rodents. And when Head and others began scraping out rodent burrows with spoons in the Carrizo Plain, they found that about 30 percent of them had cocci, while random tests of the neighboring soil could find the fungus only about 4 percent of the time.
The fungus is elusive because the microscopic filaments in the soil are invisible to the naked eye. When ground gets disturbed, those filaments can break off, sending tiny spores long distances. A 1977 California Central Valley dust storm — known as the Tempest from Tehachapi — sickened people hundreds of miles north in Sacramento.
If public health officials knew when spores were flying around, they could warn people to take precautions, wearing masks or staying inside. But finding cocci in the air is even harder than in the soil.
For 18 months starting in 2018, a network of sophisticated air filters run by the U.S. Department of Homeland Security to monitor bioterrorism threats were being used to detect cocci spores in the Phoenix area. Researchers at the Translational Genomics Research Institute, the nonprofit conducting the study, didn’t pick up any obvious patterns. A hot spot would flare up, testing positive for weeks or months, then fade to nothing. The spores’ presence varied by time and location and didn’t appear to correspond to a particular season, dust storms or the area’s midsummer monsoon — as some have assumed, said David Engelthaler, director of the institute’s infectious-disease division.
Engelthaler did find some intriguing clues. In some cases, satellite imagery showed active construction sites in the vicinity of air filters hit by spores. He also found that as temperatures increased, and soils got drier, there were more positives. This made sense to him: Ground that was baked dry would be more likely to kick up into dust if disturbed. It looked like “a hotter and drier climate,” he said, was “going to result in more exposures.”
James Markwiese, a microbiologist with the Environmental Protection Agency in Oregon, suspected that the growing wildfire footprint in the West might also be spreading spores. He knew smoke transported bacteria and fungi, and research in California found that hospital visits for Valley fever rose 20 percent following wildfires.
Cocci has never been found in wildfire smoke, but Markwiese got federal funding to look for it and teamed up with Head and other colleagues. Over a few days in September, the group flew drones affixed with tiny Teflon air filters around the rodent research site where the fungus was abundant. One drone would fly low over the ground, the rotor wash kicking up plumes of dust, while the other hovered above to catch more samples.
“Cocci sandwich,” Leda Kobziar, a University of Idaho fire scientist, said after the first attempt.
Afterward, she carefully removed the filters with tweezers inside a sterilized box. They would later be pulverized in solution and tested for cocci DNA. The team is still waiting on results. If detected here, they plan to hunt for cocci in plumes of wildfire smoke next year.
“I think that our idea of where this occurs is vastly underestimated,” Markwiese said.
Within California, the number of reported Valley fever cases has risen 800 percent from 2000 to 2022, according to the state’s department of public health. Cases have been increasing fastest in the northern part of the San Joaquin Valley as well as along the state’s southern coast. The biggest spikes happen after droughts end.
The hardy spores can survive during extreme dry stretches, Head said, then flourish into a kind of fungal superbloom during wet winters. When the ground eventually dries, spores start flying around, and cases take off. The past winter in California was one of the wettest on record. The state has been reporting about 7,000 to 9,000 cases of Valley fever over each of the past few drought-stricken years. Head predicted a spike once the rains ended California’s drought.
“I would expect that we would see over 10,000 cases in California this year,” she said.
Like ‘a fire’
Before the onslaught of snow and rain this winter, California and the West had endured one of the driest two-decade periods in more than a thousand years. Wells in the Central Valley ran dry by the hundreds. The price of water for irrigation skyrocketed, and Jace White, 33, could no longer afford to grow blueberries on a 55-acre parcel outside Fresno.
White was preparing to fallow that ground by hauling away an old storage container. The work kicked up dust from a patch of earth long undisturbed. For some reason, he lingered on the sight.
“The dirt caught my eye,” he recalled.
Three weeks later, in early April last year, he woke up in the middle of the night struggling to breathe, with a sharp pain in his left side. White’s battle with Valley fever was the most severe illness of his life. At night, he sweated torrents into his bedsheets. During the day, he lacked the strength to swipe his cellphone. Doctors punctured his back and drained nearly a gallon of fluid from his lungs. His lips cracked and his hair fell out from the antifungal treatments. He lost at least 30 pounds.
“I wouldn’t wish it on anyone,” White said.
More than half of people who get Valley fever feel no symptoms. Those who do are often misdiagnosed because symptoms — cough, fatigue, fever, night sweats — mirror other common illnesses such as pneumonia or flu. CDC officials estimate that about 500,000 people might get Valley fever annually even though reported cases hover around 20,000.
Doctors treat typical Valley fever cases with antifungal medication such as fluconazole. Many people fully recover after some weeks and become immune. There is no Valley fever vaccine for humans, but researchers are racing to develop one suitable for dogs — an effort they hope will eventually pave the way for a human one.
Within about two months, White had recovered enough to return to work. After a year, he was told he could stop taking medication. In this, he was fortunate. For 2 to 4 percent of patients, the fungus spreads out from the lungs, disseminating into the brain, spinal column or elsewhere, transforming Valley fever into a lifelong, chronic illness that cannot be cured, only managed.
Black and Filipino people have a higher risk of such severe outcomes, possibly related to genetic factors, studies have shown. Doctors say immunocompromised people and those who don’t get treated early also tend to do worse.
When McIntyre, who is Black, got sick in early 2018, he tried to tough it out, treating his worsening symptoms with turmeric home remedies and over-the-counter cold medicines. It wasn’t until lesions suddenly appeared that he went to an emergency room in Phoenix.
“One morning, I’m looking at my arm, and I’ve got these bumps all over,” he said. “And I look in the mirror, and they’re, like, all on my face.”
By that time, the fungus had expanded beyond his lungs, spreading into his bones and throughout his central nervous system. In Arizona, he had worked from home, tracking doctor visits for a health-care company, but his physical deterioration forced him to move in with his sister, then to an apartment for military veterans. It was hard for those around him to know what was wrong. He grew confused, and he staggered when he walked. Doctors at one hospital assumed he was drunk and sent him to a homeless shelter in Bakersfield.
“Imagine, this man wasn’t even drinking, and he gets labeled as an alcoholic,” said Kuran, who oversaw his emergency treatments at Kern Medical in Bakersfield.
By the time she saw him in May 2019, McIntyre could hardly speak and felt numb from the chest down. Kuran administered regular injections of amphotericin B, a powerful antifungal drug, into a plastic pouch inserted under his scalp. Despite the treatment, the inflammation around his spinal cord caused enough damage to leave him paralyzed from the waist down.
“It’s like having a fire and you’re trying to put it out,” said Kuran, who is also associate medical director at the hospital’s Valley Fever Institute. “There was nothing we could do. We gave him the maximal treatments, but the process had already started.”
When the fungus spread widely within Jose Sanchez, a plumber who worked on dusty construction sites, he began to hallucinate flocks of birds. A stroke followed, and he lost the use of his right hand. For months, he couldn’t speak. He remains unable to walk.
“Desperate,” Sanchez, 65, described himself, in Spanish, in his trailer about 80 miles east of the Carrizo Plain.
His partner, Maria Patricia Alcantara, who met Sanchez when they both worked in public health near Puebla in Mexico, quit her job at a plastics factory to care for him. She taught herself to drive so she could take him to medical appointments. Each time he needs to shower or use the bathroom, she carries him there.
Neither of them knew anything about the fungus when he got sick in 2018; they now know they can never be rid of it.
“With Valley fever, our life changed completely,” she said.
The future is here
In the summer of 2010, a 15-year-old boy crashed his all-terrain vehicle on a dirt track amid the sagebrush in Eastern Washington, scraping up his legs. The next day, he swam in the Columbia River. Before long, he developed a fever and a swollen left knee.
At the time, Valley fever was not known to exist that far north. When cases turned up, they typically involved snowbirds who had visited the Southwest. So when Heather Hill, an official in the Benton Franklin Health District, informed Washington state’s health department that this boy — and another 12-year-old who got sick around the same time — had tested positive via blood test for Valley fever but had no travel history to endemic areas, state authorities were skeptical.
“The department of health kept saying, ‘No, it’s impossible. Cocci hasn’t been seen any farther north than Northern California. You need to do a better job of interviewing,” Hill recalled. “Oh, we interviewed pretty darn good.”
Over Hill’s four-decade career as a public health nurse in a rural county, she had taken stool samples from sick cows and tested goat blood for Q fever — a bacterial infection that can spread from animals to humans — but she had never dug around in the dirt for a microscopic fungus.
“We knew it was a needle in a haystack,” she said.
But when other clues emerged, Hill and state officials put on hazmat suits and returned to the site of the crash. With hand trowels and vials, they sampled rodent holes and surface soils. But the dirt stayed in a laboratory freezer for months while the CDC developed a test to confirm whether cocci was present.
Three years had passed by the time Hill finally received a call from Tom Chiller, a CDC official, confirming cocci was growing in the soil in Washington. It would be one of the most gratifying moments of her career.
“Heather,” he told her, “you just changed our map.”
The painstaking work in Washington showed how hard it was to pinpoint where the fungus lived. Public health officials in other states, including Oregon, have tried and failed.
“It’s challenging to establish that geographic spread,” said Chiller, now the head of the CDC’s mycotic diseases branch. “But I think it’s essential if we want to communicate risk. And climate is involved in that. These fungi are inextricably linked to the environment.”
The projections that Gorris, the Los Alamos scientist, made about where cocci would spread with climate change were based on analyzing temperature and precipitation in five Southwestern states where the fungus was endemic. She concluded cocci thrived in places warmer than 51.3 degrees Fahrenheit average annual temperature with less than two feet of rain per year. When she mapped out all the places in the country with those conditions, most were in the Southwest. But three counties stood out in the Pacific Northwest: the arid swath of Eastern Washington where Hill found cocci in the ground.
“It gave us some confidence that this approach,” Gorris said, could offer “insight about where Valley fever could be endemic in the future.”
Not everyone accepts this projection. Just because spores can be blown on dust or smoke doesn’t mean they’ll survive where they land, even if soils are suitable. Genetic studies have shown separate cocci strains in different parts of the country.
“If wind were continually blowing and dispersing this, you wouldn’t be able to see those distinct populations,” said Engelthaler, of the Translational Genomics Research Institute, who has studied cocci genetics. “Everything would look mixed. And that’s not what we see.”
The genetics of the Washington cocci strain suggests it may have been there hundreds or thousands of years. But current warming trends “might be making it better for the cocci that was there to be exposed and to actually infect individuals.”
“It could be that climate trends are allowing us to actually see it now,” he said.
One early clue in Washington occurred when health officials realized that the teenage boy who crashed his ATV was not, in fact, among the first non-travel cases of Valley fever in the area. The veterinary literature showed that a horse and two dogs had gotten sick years before.
“The dogs had been a sign all along,” said Jane Sykes, a professor at the University of California at Davis’s School of Veterinary Medicine.
Valley fever is also common in animals and a particular problem for dogs that dig in the dirt.
Sykes began contacting veterinary labs across the country and eventually acquired a comprehensive trove of data: roughly 880,000 results, or nearly all the dogs tested for Valley fever across the country between 2012 and August of this year. Nearly 40 percent of them tested positive.
When Sykes and colleagues at UC Berkeley analyzed that data, they found that Valley fever cases in dogs appeared to be moving north and east out of the Southwest just in the past 10 years — essentially mimicking the spread that Gorris had predicted would take decades to play out in humans.
Dogs have been getting sick from Valley fever in Northwestern states where cocci is not known to be endemic in humans — including Oregon, Idaho, Colorado and Montana. Sykes believes the sheer quantity of cases cannot be explained solely by pets visiting the Southwest.
Sykes’s data has not yet been published, and her research is under peer review. But she has been presenting her findings to public health authorities and colleagues to spread awareness. Doctors, she said, need to be considering Valley fever far from the usual places.
“It has the potential to save people’s lives,” she said.
The dogs, with their noses in the dirt, seemed to be saying the future was already here.
‘One last test’
Over months of treatment, McIntyre regained his cognition, but it became clear he would never walk again. The paralysis has led to other complications, including urinary tract infections and kidney stones.
In the nursing home, he posts videos to TikTok from his bed, talks to relatives and attends physical therapy sessions. He knows he deserves to be angry or miserable, but he tries to keep his sense of humor.
“I’m a fun guy,” he said. “I’m filled with it.”
He tries not to get too discouraged about his health. He sees the fungus as part of God’s plan for him.
“That’s kind of why I think it may have happened to me. I could take it. God knew that,” he said. “It was one last test.”
But it was one he never saw coming. Even though he’d spent most of his life in California and Arizona, Valley fever was not something he spent time worrying about.
“I’d never heard of it,” he said.
Magda Jean-Louis contributed to this report.
About this story
Design and development by Hailey Haymond and Emily Sabens. Additional development by Yutao Chen. Editing by Katie Zezima, Olivier Laurent, Monica Ulmanu, Juliet Eilperin, Joe Moore, Emily Morman, Phil Lueck and Jay Wang.
Sources
Maps of areas in the United States that will probably reach the temperature and precipitation thresholds favorable to the spread of coccidioides are based on the methodology from “Expansion of Coccidioidomycosis Endemic Regions in the United States in Response to Climate Change” by Gorris et al. We used LOCA2 data provided by David W. Pierce at the Scripps Institution of Oceanography. The climate scenario shown is SSP245, which is comparable to the RCP4.5 warming scenario used in the original paper. Estimates of the expanded number of Valley fever cases use data published in the same study. Data on the number of Valley fever cases in California following droughts is from a 2022 study by Head et. al.